Release Notes For GenBank Release 142
GBREL.TXT Genetic Sequence Data Bank
June 15 2004
NCBI-GenBank Flat File Release 142.0
Distribution Release Notes
35532003 loci, 40325321348 bases, from 35532003 reported sequences
This document describes the format and content of the flat files that
comprise releases of the GenBank nucleotide sequence database. If you
have any questions or comments about GenBank or this document, please
contact NCBI via email at [email protected] or:
GenBank
National Center for Biotechnology Information
National Library of Medicine, 38A, 8N805
8600 Rockville Pike
Bethesda, MD 20894
USA
Phone: (301) 496-2475
Fax: (301) 480-9241
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TABLE OF CONTENTS
==========================================================================
1. INTRODUCTION
1.1 Release 142.0
1.2 Cutoff Date
1.3 Important Changes in Release 142.0
1.4 Upcoming Changes
1.5 Request for Direct Submission of Sequence Data
1.6 Organization of This Document
2. ORGANIZATION OF DATA FILES
2.1 Overview
2.2 Files
2.2.1 File Descriptions
2.2.5 File Sizes
2.2.6 Per-Division Statistics
2.2.7 Selected Per-Organism Statistics
2.2.8 Growth of GenBank
3. FILE FORMATS
3.1 File Header Information
3.2 Directory Files
3.2.1 Short Directory File
3.3 Index Files
3.3.1 Accession Number Index File
3.3.2 Keyword Phrase Index File
3.3.3 Author Name Index File
3.3.4 Journal Citation Index File
3.3.5 Gene Name Index
3.4 Sequence Entry Files
3.4.1 File Organization
3.4.2 Entry Organization
3.4.3 Sample Sequence Data File
3.4.4 LOCUS Format
3.4.5 DEFINITION Format
3.4.5.1 DEFINITION Format for NLM Entries
3.4.6 ACCESSION Format
3.4.7 VERSION Format
3.4.8 KEYWORDS Format
3.4.9 SEGMENT Format
3.4.10 SOURCE Format
3.4.11 REFERENCE Format
3.4.12 FEATURES Format
3.4.12.1 Feature Key Names
3.4.12.2 Feature Location
3.4.12.3 Feature Qualifiers
3.4.12.4 Cross-Reference Information
3.4.12.5 Feature Table Examples
3.4.13 ORIGIN Format
3.4.14 SEQUENCE Format
4. ALTERNATE RELEASES
5. KNOWN PROBLEMS OF THE GENBANK DATABASE
5.1 Incorrect Gene Symbols in Entries and Index
6. GENBANK ADMINISTRATION
6.1 Registered Trademark Notice
6.2 Citing GenBank
6.3 GenBank Distribution Formats and Media
6.4 Other Methods of Accessing GenBank Data
6.5 Request for Corrections and Comments
6.6 Credits and Acknowledgments
6.7 Disclaimer
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1. INTRODUCTION
1.1 Release 142.0
The National Center for Biotechnology Information (NCBI) at the National
Library of Medicine (NLM), National Institutes of Health (NIH) is responsible
for producing and distributing the GenBank Sequence Database. NCBI handles
all GenBank direct submissions and authors are advised to use the address
below. Submitters are encouraged to use the free Sequin software package
for sending sequence data, or the newly developed World Wide Web submission
form. See Section 1.5 below for details.
*****************************************************************************
The address for direct submissions to GenBank is:
GenBank Submissions
National Center for Biotechnology Information
Bldg 38A, Rm. 8N-803
8600 Rockville Pike
Bethesda, MD 20894
E-MAIL: [email protected]
Updates and changes to existing GenBank records:
E-MAIL: [email protected]
URL for the new GenBank submission tool - BankIt - on the World Wide Web:
http://www.ncbi.nlm.nih.gov/
(see Section 1.5 for additional details about submitting data to GenBank.)
*****************************************************************************
GenBank Release 142.0 is a release of sequence data by NCBI in the GenBank
flatfile format. GenBank is a component of a tri-partite, international
collaboration of sequence databases in the U.S., Europe, and Japan. The
collaborating databases in Europe are the European Molecular Biology Laboratory
(EMBL) at Hinxton Hall, UK, and the DNA Database of Japan (DDBJ) in Mishima,
Japan. Patent sequences are incorporated through arrangements with the
U.S. Patent and Trademark Office, and via the collaborating international
databases from other international patent offices. The database is converted
to various output formats, including the Flat File and Abstract Syntax Notation 1
(ASN.1) versions. The ASN.1 and Flat File forms of the data are available at
NCBI's anonymous FTP server: ftp.ncbi.nih.gov .
1.2 Cutoff Date
This full release, 142.0, incorporates data available to the collaborating
databases as of June 18, 2004 at approximately 1:30am EDT. For more recent
data, users are advised to:
o Download GenBank Incremental Update (GIU) files by anonymous FTP from NCBI:
ftp://ftp.ncbi.nih.gov/ncbi-asn1/daily-nc (ASN.1 format)
ftp://ftp.ncbi.nih.gov/genbank/daily-nc (flatfile format)
Mirrors of the GenBank FTP site at the NCBI are available from the San Diego
Supercomputer Center and the University of Indiana:
ftp://genbank.sdsc.edu/pub
ftp://bio-mirror.net/biomirror/genbank/
Some users who experience slow FTP transfers of large files might realize
an improvement in transfer rates from these alternate sites when traffic at
the NCBI is high.
o Use the interactive Network-Entrez or Web-Entrez applications to query
the 'Entrez: Nucleotides' database (see Section 6.4 of this document).
1.3 Important Changes in Release 142.0
1.3.1 One index file is unavailable for GenBank 142.0
A software problem prevented the generation of one of the 'index'
files which normally accompany GenBank releases:
gbjou.idx
Our apologies for any inconvenience that this might cause.
1.3.2 Organizational changes
The total number of sequence data files increased by 26 with this release:
- the EST division is now comprised of 321 files (+16)
- the GSS division is now comprised of 110 files (+6)
- the PLN division is now comprised of 12 files (+1)
- the PRI division is now comprised of 28 files (+1)
- the ROD division is now comprised of 13 files (+1)
- the STS division is now comprised of 5 files (+1)
1.3.3 **Sequence Length Limitation Removed As Of June 2004**
At the May 2003 collaborative meeting among representatives of GenBank,
EMBL, and DDBJ, it was decided that the 350 kilobase limit on the sequence
length of database records should be removed as of June 2004.
Previously, individual, complete sequences were expected to be a maximum
of 350 kbp in length. One major reason for the existence of the limit was
as an aid to users of sequence analysis software, some of which might not
be capable of processing megabase-scale sequences.
However, very significant exceptions to the 350 kbp limit have existed
for several years; Phase 1 (unordered, unoriented) and Phase 2 (ordered,
oriented) high-throughput genomic sequences (HTGS) generated by efforts
such as the Human Genome Project; large dispersed eukaryotic genes with
an intron/exon structure that spans more than 350 kbp; and sequences
which result from assemblies of Whole Genome Shotgun (WGS) project data.
Given these exceptions, and the technological advances which have made
large-scale sequencing practical for an increasing number of researchers,
the collaboration decided that the 350 kbp limit must be removed.
Software developers for some of the larger commercial sequence analysis
packages were asked in May 2003 what timeframe would be appropriate for this
change. Answers ranged from "immediately", to "several months", to "one year".
So the one-year timeframe was selected, to provide ample time to implement
changes which megabase-scale sequences might require.
As of GenBank 142.0, the length of database sequences will be limited only
by the natural structures of an organism's genome. For example, it is possible
that a single record might be used to represent all of human chromosome 1,
which is approximately 245 Mbp in length.
Some sample records with very large sequences have been made available
so that developers can test their software with them:
ftp://ftp.ncbi.nih.gov/genbank/LargeSeqs
Several changes are expected after the removal of the length limit. For
example, complete bacterial genomes (typically on the order of several
megabases) will be re-assembled into single sequence records. And the submission
process for such genomes will become much more streamlined, since database
staff will no longer have to split the genomes into pieces.
1.3.4 Rename of File 'Last.Release' and Deletion of /daily Subdirectories
The files named Last.Release, which used to be located at:
ftp://ftp.ncbi.nih.gov/genbank/daily/Last.Release
ftp://ftp.ncbi.nih.gov/ncbi-asn1/daily/Last.Release
contain the number of the GenBank release which is currently installed
on the NCBI FTP site. As of Release 142.0 in June 2004, these files have
been moved and renamed as:
ftp://ftp.ncbi.nih.gov/genbank/GB_Release_Number
ftp://ftp.ncbi.nih.gov/ncbi-asn1/GB_Release_Number
The /daily subdirectories, which had been used for cumulative update
products that are no longer supported, have been deleted.
1.3.3 GSS File Header Problem
GSS sequences at GenBank are maintained in one of two different systems,
depending on their origin. One recent change to release processing involves
the parallelization of the dumps from those systems. Because the second dump
(for example) has no prior knowledge of exactly how many GSS files will be
dumped from the first, it doesn't know how to number it's own output files.
There is thus a discrepancy between the filenames and file headers for
eighteen GSS flatfiles in Release 142.0. Consider the gbgss93.seq file:
GBGSS1.SEQ Genetic Sequence Data Bank
June 15 2004
NCBI-GenBank Flat File Release 142.0
GSS Sequences (Part 1)
88249 loci, 65635082 bases, from 88249 reported sequences
Here, the filename and part number in the header is "1", though the file
has been renamed as "93" based on the files dumped from the other system.
We will work to resolve this discrepancy in future releases, but the
priority is certainly much lower than many other tasks.
1.4 Upcoming Changes
1.4.1 New qualifier : /old_locus_tag
The /locus_tag qualifier was introduced in April 2003 to provide
a method for systematically identifying genes, coding regions and
other features which typically result from computational analysis.
This qualifier is typically used instead of /gene .
Sometimes the /locus_tag identifier series supplied by a submitter
of sequence data undergoes a change. Because the original /locus_tag
identifiers might be referenced in journal articles, or in databases,
a method of preserving the original identifiers is needed.
A new qualifier, /old_locus_tag , will be introduced as of October
2004 for this purpose. A formal description of the qualifier will be
made available via upcoming GenBank release notes, and via the GenBank
newsgroup.
1.4.2 New type of gap() operator
CON-division records utilize a CONTIG line with a join() statement,
which specifies how sequences can be combined to form a much larger
object. For example:
LOCUS AE016959 23508449 bp DNA linear CON 12-JUN-2003
DEFINITION Oryza sativa (japonica cultivar-group) chromosome 10, complete
sequence.
ACCESSION AE016959
[....]
CONTIG join(AE017047.1:1..300029,AE017048.1:61..300029,
AE017049.1:61..304564,AE017050.1:61..302504,AE017051.1:61..300029,
AE017052.1:61..300029,AE017053.1:61..303511,AE017054.1:61..302085,
AE017055.1:61..300029,AE017056.1:61..300029,AE017057.1:61..300029,
AE017058.1:61..300029,AE017059.1:61..300029,AE017060.1:61..95932,
gap(30001),AE017061.1:1..300028,AE017062.1:61..306096,
[....]
A gap operator is legal in these join statements. 'gap()' indicates a gap
of unknown length. 'gap(N)', where 'N' is a positive integer, indicates a gap
with a physically-estimated length of 'N' bases.
In some sequencing projects, a convention is agreed upon by which gaps
of unknown length are all represented by a uniform value, such as 100.
To capture this usage, a new type of gap operator will be legal as of
October 2004 : 'gap(unkN)', where 'N' is a positive integer. For a gap of
length 100, utilized by convention rather than reflective of the gap's
actual size, the operator would be:
gap(unk100)
This new gap operator will make clear the distinction between a
gap with a physically-estimated length, and a gap with a length that
has no actual physical basis. Further details about this new operator
will be made available via these release notes and the GenBank newsgroup.
1.4.3 New /compare qualifier
Four different features exist which can be used to annotate regions
of sequence that are either uncertain or that differ in comparison
to some other sequence:
variation
conflict
misc_difference
old_sequence
A /citation qualifier is used to refer to a publication that details
the nature of the uncertain or differing bases. However, a publication
may not always be available (unpublished references), and simply
referring to a publication is quite indirect.
The new /compare qualifer will provide a method for directly
referencing a base range on a record that exhibits a sequence
difference:
/compare="Accession.Version:X..Y"
For example:
/compare="M10101.1:1..5"
A formal description of /compare will be made available via upcoming
GenBank release notes, and via the GenBank newsgroup.
1.5 Request for Direct Submission of Sequence Data
A successful GenBank requires that sequence data enter the database as
soon as possible after publication, that the annotations be as complete as
possible, and that the sequence and annotation data be accurate. All
three of these requirements are best met if authors of sequence data
submit their data directly to GenBank in a usable form. It is especially
important that these submissions be in computer-readable form.
GenBank must rely on direct author submission of data to ensure that
it achieves its goals of completeness, accuracy, and timeliness. To
assist researchers in entering their own sequence data, GenBank
provides a WWW submission tool called BankIt, as well as a stand-alone
software package called Sequin. BankIt and Sequin are both easy-to-use
programs that enable authors to enter a sequence, annotate it, and
submit it to GenBank. Through the international collaboration of DNA
sequence databases, GenBank submissions are forwarded daily for inclusion
in the EMBL and DDBJ databases.
SEQUIN. Sequin is an interactive, graphically-oriented program based
on screen forms and controlled vocabularies that guides you through the
process of entering your sequence and providing biological and
bibliographic annotation. Sequin is designed to simplify the sequence submission
process, and to provide increased data handling capabilities to accomodate
very long sequences, complex annotations, and robust error checking. E-mail
the completed submission file to : [email protected]
Sequin is provided for Macintosh, PC/Windows, UNIX and VMS computers.
It is available by annonymous ftp from ftp.ncbi.nih.gov; login as
anonymous and use your e-mail address as the password. It is located in
the sequin directory. Or direct your web browser to this URL:
ftp://ftp.ncbi.nih.gov/sequin
BANKIT. BankIt provides a simple forms approach for submitting your
sequence and descriptive information to GenBank. Your submission will
be submitted directly to GenBank via the World Wide Web, and
immediately forwarded for inclusion in the EMBL and DDBJ databases.
BankIt may be used with Netscape, Internet Explorer, and other common
WWW clients. You can access BankIt from GenBank's home page:
http://www.ncbi.nlm.nih.gov/
AUTHORIN. Authorin sequence submissions are no longer accepted by
GenBank, and the Authorin application is no longer distributed by NCBI.
If you have questions about GenBank submissions or any of the data
submission tools, contact NCBI at: [email protected] or 301-496-2475.
1.6 Organization of This Document
The second section describes the contents of GenBank releases. The third
section illustrates the formats of the flat files. The fourth section
describes other versions of the data, the fifth section identifies known prob-
lems, and the sixth contains administrative details.
2. ORGANIZATION OF DATA FILES
2.1 Overview
GenBank releases consist of a set of ASCII text files, most of which
contain sequence data. A few supplemental "index" files are also supplied,
containing comprehensive lists of author names, journal citations,
gene names, and keywords, along with the accession numbers of the records
in which they can be found (see Section 3.3). The line-lengths of
these files is variable.
2.2 Files
This GenBank flat file release consists of 634 files. The lists
that follow describe each of the files included in the distribution.
Their sizes and base pair content are also summarized.
2.2.1 File Descriptions
As outlined in Section 1.3.1, the following file is unavailable
for GenBank Release 142.0 :
gbjou.idx - Index of the entries according to journal citation.
Files included in this release are:
1. gbrel.txt - Release notes (this document).
2. gbsdr.txt - Short directory of the data bank.
3. gbacc.idx - Index of the entries according to accession number.
4. gbkey.idx - Index of the entries according to keyword phrase.
5. gbaut1.idx - Index of the entries according to author, part 1.
6. gbaut2.idx - Index of the entries according to author, part 2.
7. gbaut3.idx - Index of the entries according to author, part 3.
8. gbaut4.idx - Index of the entries according to author, part 4.
9. gbaut5.idx - Index of the entries according to author, part 5.
10. gbaut6.idx - Index of the entries according to author, part 6.
11. gbaut7.idx - Index of the entries according to author, part 7.
12. gbaut8.idx - Index of the entries according to author, part 8.
13. gbaut9.idx - Index of the entries according to author, part 9.
14. gbaut10.idx - Index of the entries according to author, part 10.
15. gbaut11.idx - Index of the entries according to author, part 11.
16. gbaut12.idx - Index of the entries according to author, part 12.
17. gbaut13.idx - Index of the entries according to author, part 13.
18. gbaut14.idx - Index of the entries according to author, part 14.
19. gbaut15.idx - Index of the entries according to author, part 15.
20. gbaut16.idx - Index of the entries according to author, part 16.
21. gbaut17.idx - Index of the entries according to author, part 17.
22. gbaut18.idx - Index of the entries according to author, part 18.
23. gbaut19.idx - Index of the entries according to author, part 19.
24. gbaut20.idx - Index of the entries according to author, part 20.
25. gbaut21.idx - Index of the entries according to author, part 21.
26. gbaut22.idx - Index of the entries according to author, part 22.
27. gbaut23.idx - Index of the entries according to author, part 23.
28. gbaut24.idx - Index of the entries according to author, part 24.
29. gbaut25.idx - Index of the entries according to author, part 25.
30. gbgen.idx - Index of the entries according to gene names.
31. gbsec.idx - Index of the entries according to secondary accession number.
32. gbpri1.seq - Primate sequence entries, part 1.
33. gbpri2.seq - Primate sequence entries, part 2.
34. gbpri3.seq - Primate sequence entries, part 3.
35. gbpri4.seq - Primate sequence entries, part 4.
36. gbpri5.seq - Primate sequence entries, part 5.
37. gbpri6.seq - Primate sequence entries, part 6.
38. gbpri7.seq - Primate sequence entries, part 7.
39. gbpri8.seq - Primate sequence entries, part 8.
40. gbpri9.seq - Primate sequence entries, part 9.
41. gbpri10.seq - Primate sequence entries, part 10.
42. gbpri11.seq - Primate sequence entries, part 11.
43. gbpri12.seq - Primate sequence entries, part 12.
44. gbpri13.seq - Primate sequence entries, part 13.
45. gbpri14.seq - Primate sequence entries, part 14.
46. gbpri15.seq - Primate sequence entries, part 15.
47. gbpri16.seq - Primate sequence entries, part 16.
48. gbpri17.seq - Primate sequence entries, part 17.
49. gbpri18.seq - Primate sequence entries, part 18.
50. gbpri19.seq - Primate sequence entries, part 19.
51. gbpri20.seq - Primate sequence entries, part 20.
52. gbpri21.seq - Primate sequence entries, part 21.
53. gbpri22.seq - Primate sequence entries, part 22.
54. gbpri23.seq - Primate sequence entries, part 23.
55. gbpri24.seq - Primate sequence entries, part 24.
56. gbpri25.seq - Primate sequence entries, part 25.
57. gbpri26.seq - Primate sequence entries, part 26.
58. gbpri27.seq - Primate sequence entries, part 27.
59. gbpri28.seq - Primate sequence entries, part 28.
60. gbrod1.seq - Rodent sequence entries, part 1.
61. gbrod2.seq - Rodent sequence entries, part 2.
62. gbrod3.seq - Rodent sequence entries, part 3.
63. gbrod4.seq - Rodent sequence entries, part 4.
64. gbrod5.seq - Rodent sequence entries, part 5.
65. gbrod6.seq - Rodent sequence entries, part 6.
66. gbrod7.seq - Rodent sequence entries, part 7.
67. gbrod8.seq - Rodent sequence entries, part 8.
68. gbrod9.seq - Rodent sequence entries, part 9.
69. gbrod10.seq - Rodent sequence entries, part 10.
70. gbrod11.seq - Rodent sequence entries, part 11.
71. gbrod12.seq - Rodent sequence entries, part 12.
72. gbrod13.seq - Rodent sequence entries, part 13.
73. gbmam.seq - Other mammalian sequence entries.
74. gbvrt1.seq - Other vertebrate sequence entries, part 1.
75. gbvrt2.seq - Other vertebrate sequence entries, part 2.
76. gbvrt3.seq - Other vertebrate sequence entries, part 3.
77. gbvrt4.seq - Other vertebrate sequence entries, part 4.
78. gbvrt5.seq - Other vertebrate sequence entries, part 5.
79. gbvrt6.seq - Other vertebrate sequence entries, part 5.
80. gbinv1.seq - Invertebrate sequence entries, part 1.
81. gbinv2.seq - Invertebrate sequence entries, part 2.
82. gbinv3.seq - Invertebrate sequence entries, part 3.
83. gbinv4.seq - Invertebrate sequence entries, part 4.
84. gbinv5.seq - Invertebrate sequence entries, part 5.
85. gbinv6.seq - Invertebrate sequence entries, part 6.
86. gbpln1.seq - Plant sequence entries (including fungi and algae), part 1.
87. gbpln2.seq - Plant sequence entries (including fungi and algae), part 2.
88. gbpln3.seq - Plant sequence entries (including fungi and algae), part 3.
89. gbpln4.seq - Plant sequence entries (including fungi and algae), part 4.
90. gbpln5.seq - Plant sequence entries (including fungi and algae), part 5.
91. gbpln6.seq - Plant sequence entries (including fungi and algae), part 6.
92. gbpln7.seq - Plant sequence entries (including fungi and algae), part 7.
93. gbpln8.seq - Plant sequence entries (including fungi and algae), part 8.
94. gbpln9.seq - Plant sequence entries (including fungi and algae), part 9.
95. gbpln10.seq - Plant sequence entries (including fungi and algae), part 10.
96. gbpln11.seq - Plant sequence entries (including fungi and algae), part 11.
97. gbpln12.seq - Plant sequence entries (including fungi and algae), part 12.
98. gbbct1.seq - Bacterial sequence entries, part 1.
99. gbbct2.seq - Bacterial sequence entries, part 2.
100. gbbct3.seq - Bacterial sequence entries, part 3.
101. gbbct4.seq - Bacterial sequence entries, part 4.
102. gbbct5.seq - Bacterial sequence entries, part 5.
103. gbbct6.seq - Bacterial sequence entries, part 6.
104. gbbct7.seq - Bacterial sequence entries, part 7.
105. gbbct8.seq - Bacterial sequence entries, part 8.
106. gbbct9.seq - Bacterial sequence entries, part 9.
107. gbvrl1.seq - Viral sequence entries, part 1.
108. gbvrl2.seq - Viral sequence entries, part 2.
109. gbvrl3.seq - Viral sequence entries, part 3.
110. gbvrl4.seq - Viral sequence entries, part 4.
111. gbphg.seq - Phage sequence entries.
112. gbsyn.seq - Synthetic and chimeric sequence entries.
113. gbuna.seq - Unannotated sequence entries.
114. gbest1.seq - EST (expressed sequence tag) sequence entries, part 1.
115. gbest2.seq - EST (expressed sequence tag) sequence entries, part 2.
116. gbest3.seq - EST (expressed sequence tag) sequence entries, part 3.
117. gbest4.seq - EST (expressed sequence tag) sequence entries, part 4.
118. gbest5.seq - EST (expressed sequence tag) sequence entries, part 5.
119. gbest6.seq - EST (expressed sequence tag) sequence entries, part 6.
120. gbest7.seq - EST (expressed sequence tag) sequence entries, part 7.
121. gbest8.seq - EST (expressed sequence tag) sequence entries, part 8.
122. gbest9.seq - EST (expressed sequence tag) sequence entries, part 9.
123. gbest10.seq - EST (expressed sequence tag) sequence entries, part 10.
124. gbest11.seq - EST (expressed sequence tag) sequence entries, part 11.
125. gbest12.seq - EST (expressed sequence tag) sequence entries, part 12.
126. gbest13.seq - EST (expressed sequence tag) sequence entries, part 13.
127. gbest14.seq - EST (expressed sequence tag) sequence entries, part 14.
128. gbest15.seq - EST (expressed sequence tag) sequence entries, part 15.
129. gbest16.seq - EST (expressed sequence tag) sequence entries, part 16.
130. gbest17.seq - EST (expressed sequence tag) sequence entries, part 17.
131. gbest18.seq - EST (expressed sequence tag) sequence entries, part 18.
132. gbest19.seq - EST (expressed sequence tag) sequence entries, part 19.
133. gbest20.seq - EST (expressed sequence tag) sequence entries, part 20.
134. gbest21.seq - EST (expressed sequence tag) sequence entries, part 21.
135. gbest22.seq - EST (expressed sequence tag) sequence entries, part 22.
136. gbest23.seq - EST (expressed sequence tag) sequence entries, part 23.
137. gbest24.seq - EST (expressed sequence tag) sequence entries, part 24.
138. gbest25.seq - EST (expressed sequence tag) sequence entries, part 25.
139. gbest26.seq - EST (expressed sequence tag) sequence entries, part 26.
140. gbest27.seq - EST (expressed sequence tag) sequence entries, part 27.
141. gbest28.seq - EST (expressed sequence tag) sequence entries, part 28.
142. gbest29.seq - EST (expressed sequence tag) sequence entries, part 29.
143. gbest30.seq - EST (expressed sequence tag) sequence entries, part 30.
144. gbest31.seq - EST (expressed sequence tag) sequence entries, part 31.
145. gbest32.seq - EST (expressed sequence tag) sequence entries, part 32.
146. gbest33.seq - EST (expressed sequence tag) sequence entries, part 33.
147. gbest34.seq - EST (expressed sequence tag) sequence entries, part 34.
148. gbest35.seq - EST (expressed sequence tag) sequence entries, part 35.
149. gbest36.seq - EST (expressed sequence tag) sequence entries, part 36.
150. gbest37.seq - EST (expressed sequence tag) sequence entries, part 37.
151. gbest38.seq - EST (expressed sequence tag) sequence entries, part 38.
152. gbest39.seq - EST (expressed sequence tag) sequence entries, part 39.
153. gbest40.seq - EST (expressed sequence tag) sequence entries, part 40.
154. gbest41.seq - EST (expressed sequence tag) sequence entries, part 41.
155. gbest42.seq - EST (expressed sequence tag) sequence entries, part 42.
156. gbest43.seq - EST (expressed sequence tag) sequence entries, part 43.
157. gbest44.seq - EST (expressed sequence tag) sequence entries, part 44.
158. gbest45.seq - EST (expressed sequence tag) sequence entries, part 45.
159. gbest46.seq - EST (expressed sequence tag) sequence entries, part 46.
160. gbest47.seq - EST (expressed sequence tag) sequence entries, part 47.
161. gbest48.seq - EST (expressed sequence tag) sequence entries, part 48.
162. gbest49.seq - EST (expressed sequence tag) sequence entries, part 49.
163. gbest50.seq - EST (expressed sequence tag) sequence entries, part 50.
164. gbest51.seq - EST (expressed sequence tag) sequence entries, part 51.
165. gbest52.seq - EST (expressed sequence tag) sequence entries, part 52.
166. gbest53.seq - EST (expressed sequence tag) sequence entries, part 53.
167. gbest54.seq - EST (expressed sequence tag) sequence entries, part 54.
168. gbest55.seq - EST (expressed sequence tag) sequence entries, part 55.
169. gbest56.seq - EST (expressed sequence tag) sequence entries, part 56.
170. gbest57.seq - EST (expressed sequence tag) sequence entries, part 57.
171. gbest58.seq - EST (expressed sequence tag) sequence entries, part 58.
172. gbest59.seq - EST (expressed sequence tag) sequence entries, part 59.
173. gbest60.seq - EST (expressed sequence tag) sequence entries, part 60.
174. gbest61.seq - EST (expressed sequence tag) sequence entries, part 61.
175. gbest62.seq - EST (expressed sequence tag) sequence entries, part 62.
176. gbest63.seq - EST (expressed sequence tag) sequence entries, part 63.
177. gbest64.seq - EST (expressed sequence tag) sequence entries, part 64.
178. gbest65.seq - EST (expressed sequence tag) sequence entries, part 65.
179. gbest66.seq - EST (expressed sequence tag) sequence entries, part 66.
180. gbest67.seq - EST (expressed sequence tag) sequence entries, part 67.
181. gbest68.seq - EST (expressed sequence tag) sequence entries, part 68.
182. gbest69.seq - EST (expressed sequence tag) sequence entries, part 69.
183. gbest70.seq - EST (expressed sequence tag) sequence entries, part 70.
184. gbest71.seq - EST (expressed sequence tag) sequence entries, part 71.
185. gbest72.seq - EST (expressed sequence tag) sequence entries, part 72.
186. gbest73.seq - EST (expressed sequence tag) sequence entries, part 73.
187. gbest74.seq - EST (expressed sequence tag) sequence entries, part 74.
188. gbest75.seq - EST (expressed sequence tag) sequence entries, part 75.
189. gbest76.seq - EST (expressed sequence tag) sequence entries, part 76.
190. gbest77.seq - EST (expressed sequence tag) sequence entries, part 77.
191. gbest78.seq - EST (expressed sequence tag) sequence entries, part 78.
192. gbest79.seq - EST (expressed sequence tag) sequence entries, part 79.
193. gbest80.seq - EST (expressed sequence tag) sequence entries, part 80.
194. gbest81.seq - EST (expressed sequence tag) sequence entries, part 81.
195. gbest82.seq - EST (expressed sequence tag) sequence entries, part 82.
196. gbest83.seq - EST (expressed sequence tag) sequence entries, part 83.
197. gbest84.seq - EST (expressed sequence tag) sequence entries, part 84.
198. gbest85.seq - EST (expressed sequence tag) sequence entries, part 85.
199. gbest86.seq - EST (expressed sequence tag) sequence entries, part 86.
200. gbest87.seq - EST (expressed sequence tag) sequence entries, part 87.
201. gbest88.seq - EST (expressed sequence tag) sequence entries, part 88.
202. gbest89.seq - EST (expressed sequence tag) sequence entries, part 89
203. gbest90.seq - EST (expressed sequence tag) sequence entries, part 90.
204. gbest91.seq - EST (expressed sequence tag) sequence entries, part 91.
205. gbest92.seq - EST (expressed sequence tag) sequence entries, part 92.
206. gbest93.seq - EST (expressed sequence tag) sequence entries, part 93.
207. gbest94.seq - EST (expressed sequence tag) sequence entries, part 94.
208. gbest95.seq - EST (expressed sequence tag) sequence entries, part 95.
209. gbest96.seq - EST (expressed sequence tag) sequence entries, part 96.
210. gbest97.seq - EST (expressed sequence tag) sequence entries, part 97.
211. gbest98.seq - EST (expressed sequence tag) sequence entries, part 98.
212. gbest99.seq - EST (expressed sequence tag) sequence entries, part 99.
213. gbest100.seq - EST (expressed sequence tag) sequence entries, part 100.
214. gbest101.seq - EST (expressed sequence tag) sequence entries, part 101.
215. gbest102.seq - EST (expressed sequence tag) sequence entries, part 102.
216. gbest103.seq - EST (expressed sequence tag) sequence entries, part 103.
217. gbest104.seq - EST (expressed sequence tag) sequence entries, part 104.
218. gbest105.seq - EST (expressed sequence tag) sequence entries, part 105.
219. gbest106.seq - EST (expressed sequence tag) sequence entries, part 106.
220. gbest107.seq - EST (expressed sequence tag) sequence entries, part 107.
221. gbest108.seq - EST (expressed sequence tag) sequence entries, part 108.
222. gbest109.seq - EST (expressed sequence tag) sequence entries, part 109.
223. gbest110.seq - EST (expressed sequence tag) sequence entries, part 110.
224. gbest111.seq - EST (expressed sequence tag) sequence entries, part 111.
225. gbest112.seq - EST (expressed sequence tag) sequence entries, part 112.
226. gbest113.seq - EST (expressed sequence tag) sequence entries, part 113.
227. gbest114.seq - EST (expressed sequence tag) sequence entries, part 114.
228. gbest115.seq - EST (expressed sequence tag) sequence entries, part 115.
229. gbest116.seq - EST (expressed sequence tag) sequence entries, part 116.
230. gbest117.seq - EST (expressed sequence tag) sequence entries, part 117.
231. gbest118.seq - EST (expressed sequence tag) sequence entries, part 118.
232. gbest119.seq - EST (expressed sequence tag) sequence entries, part 119.
233. gbest120.seq - EST (expressed sequence tag) sequence entries, part 120.
234. gbest121.seq - EST (expressed sequence tag) sequence entries, part 121.
235. gbest122.seq - EST (expressed sequence tag) sequence entries, part 122.
236. gbest123.seq - EST (expressed sequence tag) sequence entries, part 123.
237. gbest124.seq - EST (expressed sequence tag) sequence entries, part 124.
238. gbest125.seq - EST (expressed sequence tag) sequence entries, part 125.
239. gbest126.seq - EST (expressed sequence tag) sequence entries, part 126.
240. gbest127.seq - EST (expressed sequence tag) sequence entries, part 127.
241. gbest128.seq - EST (expressed sequence tag) sequence entries, part 128.
242. gbest129.seq - EST (expressed sequence tag) sequence entries, part 129.
243. gbest130.seq - EST (expressed sequence tag) sequence entries, part 130.
244. gbest131.seq - EST (expressed sequence tag) sequence entries, part 131.
245. gbest132.seq - EST (expressed sequence tag) sequence entries, part 132.
246. gbest133.seq - EST (expressed sequence tag) sequence entries, part 133.
247. gbest134.seq - EST (expressed sequence tag) sequence entries, part 134.
248. gbest135.seq - EST (expressed sequence tag) sequence entries, part 135.
249. gbest136.seq - EST (expressed sequence tag) sequence entries, part 136.
250. gbest137.seq - EST (expressed sequence tag) sequence entries, part 137.
251. gbest138.seq - EST (expressed sequence tag) sequence entries, part 138.
252. gbest139.seq - EST (expressed sequence tag) sequence entries, part 139.
253. gbest140.seq - EST (expressed sequence tag) sequence entries, part 140.
254. gbest141.seq - EST (expressed sequence tag) sequence entries, part 141.
255. gbest142.seq - EST (expressed sequence tag) sequence entries, part 142.
256. gbest143.seq - EST (expressed sequence tag) sequence entries, part 143.
257. gbest144.seq - EST (expressed sequence tag) sequence entries, part 144.
258. gbest145.seq - EST (expressed sequence tag) sequence entries, part 145.
259. gbest146.seq - EST (expressed sequence tag) sequence entries, part 146.
260. gbest147.seq - EST (expressed sequence tag) sequence entries, part 147.
261. gbest148.seq - EST (expressed sequence tag) sequence entries, part 148.
262. gbest149.seq - EST (expressed sequence tag) sequence entries, part 149.
263. gbest150.seq - EST (expressed sequence tag) sequence entries, part 150.
264. gbest151.seq - EST (expressed sequence tag) sequence entries, part 151.
265. gbest152.seq - EST (expressed sequence tag) sequence entries, part 152.
266. gbest153.seq - EST (expressed sequence tag) sequence entries, part 153.
267. gbest154.seq - EST (expressed sequence tag) sequence entries, part 154.
268. gbest155.seq - EST (expressed sequence tag) sequence entries, part 155.
269. gbest156.seq - EST (expressed sequence tag) sequence entries, part 156.
270. gbest157.seq - EST (expressed sequence tag) sequence entries, part 157.
271. gbest158.seq - EST (expressed sequence tag) sequence entries, part 158.
272. gbest159.seq - EST (expressed sequence tag) sequence entries, part 159.
273. gbest160.seq - EST (expressed sequence tag) sequence entries, part 160.
274. gbest161.seq - EST (expressed sequence tag) sequence entries, part 161.
275. gbest162.seq - EST (expressed sequence tag) sequence entries, part 162.
276. gbest163.seq - EST (expressed sequence tag) sequence entries, part 163.
277. gbest164.seq - EST (expressed sequence tag) sequence entries, part 164.
278. gbest165.seq - EST (expressed sequence tag) sequence entries, part 165.
279. gbest166.seq - EST (expressed sequence tag) sequence entries, part 166.
280. gbest167.seq - EST (expressed sequence tag) sequence entries, part 167.
281. gbest168.seq - EST (expressed sequence tag) sequence entries, part 168.
282. gbest169.seq - EST (expressed sequence tag) sequence entries, part 169.
283. gbest170.seq - EST (expressed sequence tag) sequence entries, part 170.
284. gbest171.seq - EST (expressed sequence tag) sequence entries, part 171.
285. gbest172.seq - EST (expressed sequence tag) sequence entries, part 172.
286. gbest173.seq - EST (expressed sequence tag) sequence entries, part 173.
287. gbest174.seq - EST (expressed sequence tag) sequence entries, part 174.
288. gbest175.seq - EST (expressed sequence tag) sequence entries, part 175.
289. gbest176.seq - EST (expressed sequence tag) sequence entries, part 176.
290. gbest177.seq - EST (expressed sequence tag) sequence entries, part 177.
291. gbest178.seq - EST (expressed sequence tag) sequence entries, part 178.
292. gbest179.seq - EST (expressed sequence tag) sequence entries, part 179.
293. gbest180.seq - EST (expressed sequence tag) sequence entries, part 180.
294. gbest181.seq - EST (expressed sequence tag) sequence entries, part 181.
295. gbest182.seq - EST (expressed sequence tag) sequence entries, part 182.
296. gbest183.seq - EST (expressed sequence tag) sequence entries, part 183.
297. gbest184.seq - EST (expressed sequence tag) sequence entries, part 184.
298. gbest185.seq - EST (expressed sequence tag) sequence entries, part 185.
299. gbest186.seq - EST (expressed sequence tag) sequence entries, part 186.
300. gbest187.seq - EST (expressed sequence tag) sequence entries, part 187.
301. gbest188.seq - EST (expressed sequence tag) sequence entries, part 188.
302. gbest189.seq - EST (expressed sequence tag) sequence entries, part 189.
303. gbest190.seq - EST (expressed sequence tag) sequence entries, part 190.
304. gbest191.seq - EST (expressed sequence tag) sequence entries, part 191.
305. gbest192.seq - EST (expressed sequence tag) sequence entries, part 192.
306. gbest193.seq - EST (expressed sequence tag) sequence entries, part 193.
307. gbest194.seq - EST (expressed sequence tag) sequence entries, part 194.
308. gbest195.seq - EST (expressed sequence tag) sequence entries, part 195.
309. gbest196.seq - EST (expressed sequence tag) sequence entries, part 196.
310. gbest197.seq - EST (expressed sequence tag) sequence entries, part 197.
311. gbest198.seq - EST (expressed sequence tag) sequence entries, part 198.
312. gbest199.seq - EST (expressed sequence tag) sequence entries, part 199.
313. gbest200.seq - EST (expressed sequence tag) sequence entries, part 200.
314. gbest201.seq - EST (expressed sequence tag) sequence entries, part 201.
315. gbest202.seq - EST (expressed sequence tag) sequence entries, part 202.
316. gbest203.seq - EST (expressed sequence tag) sequence entries, part 203.
317. gbest204.seq - EST (expressed sequence tag) sequence entries, part 204.
318. gbest205.seq - EST (expressed sequence tag) sequence entries, part 205.
319. gbest206.seq - EST (expressed sequence tag) sequence entries, part 206.
320. gbest207.seq - EST (expressed sequence tag) sequence entries, part 207.
321. gbest208.seq - EST (expressed sequence tag) sequence entries, part 208.
322. gbest209.seq - EST (expressed sequence tag) sequence entries, part 209.
323. gbest210.seq - EST (expressed sequence tag) sequence entries, part 210.
324. gbest211.seq - EST (expressed sequence tag) sequence entries, part 211.
325. gbest212.seq - EST (expressed sequence tag) sequence entries, part 212.
326. gbest213.seq - EST (expressed sequence tag) sequence entries, part 213.
327. gbest214.seq - EST (expressed sequence tag) sequence entries, part 214.
328. gbest215.seq - EST (expressed sequence tag) sequence entries, part 215.
329. gbest216.seq - EST (expressed sequence tag) sequence entries, part 216.
330. gbest217.seq - EST (expressed sequence tag) sequence entries, part 217.
331. gbest218.seq - EST (expressed sequence tag) sequence entries, part 218.
332. gbest219.seq - EST (expressed sequence tag) sequence entries, part 219.
333. gbest220.seq - EST (expressed sequence tag) sequence entries, part 220.
334. gbest221.seq - EST (expressed sequence tag) sequence entries, part 221.
335. gbest222.seq - EST (expressed sequence tag) sequence entries, part 222.
336. gbest223.seq - EST (expressed sequence tag) sequence entries, part 223.
337. gbest224.seq - EST (expressed sequence tag) sequence entries, part 224.
338. gbest225.seq - EST (expressed sequence tag) sequence entries, part 225.
339. gbest226.seq - EST (expressed sequence tag) sequence entries, part 226.
340. gbest227.seq - EST (expressed sequence tag) sequence entries, part 227.
341. gbest228.seq - EST (expressed sequence tag) sequence entries, part 228.
342. gbest229.seq - EST (expressed sequence tag) sequence entries, part 229.
343. gbest230.seq - EST (expressed sequence tag) sequence entries, part 230.
344. gbest231.seq - EST (expressed sequence tag) sequence entries, part 231.
345. gbest232.seq - EST (expressed sequence tag) sequence entries, part 232.
346. gbest233.seq - EST (expressed sequence tag) sequence entries, part 233.
347. gbest234.seq - EST (expressed sequence tag) sequence entries, part 234.
348. gbest235.seq - EST (expressed sequence tag) sequence entries, part 235.
349. gbest236.seq - EST (expressed sequence tag) sequence entries, part 236.
350. gbest237.seq - EST (expressed sequence tag) sequence entries, part 237.
351. gbest238.seq - EST (expressed sequence tag) sequence entries, part 238.
352. gbest239.seq - EST (expressed sequence tag) sequence entries, part 239.
353. gbest240.seq - EST (expressed sequence tag) sequence entries, part 240.
354. gbest241.seq - EST (expressed sequence tag) sequence entries, part 241.
355. gbest242.seq - EST (expressed sequence tag) sequence entries, part 242.
356. gbest243.seq - EST (expressed sequence tag) sequence entries, part 243.
357. gbest244.seq - EST (expressed sequence tag) sequence entries, part 244.
358. gbest245.seq - EST (expressed sequence tag) sequence entries, part 245.
359. gbest246.seq - EST (expressed sequence tag) sequence entries, part 246.
360. gbest247.seq - EST (expressed sequence tag) sequence entries, part 247.
361. gbest248.seq - EST (expressed sequence tag) sequence entries, part 248.
362. gbest249.seq - EST (expressed sequence tag) sequence entries, part 249.
363. gbest250.seq - EST (expressed sequence tag) sequence entries, part 250.
364. gbest251.seq - EST (expressed sequence tag) sequence entries, part 251.
365. gbest252.seq - EST (expressed sequence tag) sequence entries, part 252.
366. gbest253.seq - EST (expressed sequence tag) sequence entries, part 253.
367. gbest254.seq - EST (expressed sequence tag) sequence entries, part 254.
368. gbest255.seq - EST (expressed sequence tag) sequence entries, part 255.
369. gbest256.seq - EST (expressed sequence tag) sequence entries, part 256.
370. gbest257.seq - EST (expressed sequence tag) sequence entries, part 257.
371. gbest258.seq - EST (expressed sequence tag) sequence entries, part 258.
372. gbest259.seq - EST (expressed sequence tag) sequence entries, part 259.
373. gbest260.seq - EST (expressed sequence tag) sequence entries, part 260.
374. gbest261.seq - EST (expressed sequence tag) sequence entries, part 261.
375. gbest262.seq - EST (expressed sequence tag) sequence entries, part 262.
376. gbest263.seq - EST (expressed sequence tag) sequence entries, part 263.
377. gbest264.seq - EST (expressed sequence tag) sequence entries, part 264.
378. gbest265.seq - EST (expressed sequence tag) sequence entries, part 265.
379. gbest266.seq - EST (expressed sequence tag) sequence entries, part 266.
380. gbest267.seq - EST (expressed sequence tag) sequence entries, part 267.
381. gbest268.seq - EST (expressed sequence tag) sequence entries, part 268.
382. gbest269.seq - EST (expressed sequence tag) sequence entries, part 269.
383. gbest270.seq - EST (expressed sequence tag) sequence entries, part 270.
384. gbest271.seq - EST (expressed sequence tag) sequence entries, part 271.
385. gbest272.seq - EST (expressed sequence tag) sequence entries, part 272.
386. gbest273.seq - EST (expressed sequence tag) sequence entries, part 273.
387. gbest274.seq - EST (expressed sequence tag) sequence entries, part 274.
388. gbest275.seq - EST (expressed sequence tag) sequence entries, part 275.
389. gbest276.seq - EST (expressed sequence tag) sequence entries, part 276.
390. gbest277.seq - EST (expressed sequence tag) sequence entries, part 277.
391. gbest278.seq - EST (expressed sequence tag) sequence entries, part 278.
392. gbest279.seq - EST (expressed sequence tag) sequence entries, part 279.
393. gbest280.seq - EST (expressed sequence tag) sequence entries, part 280.
394. gbest281.seq - EST (expressed sequence tag) sequence entries, part 281.
395. gbest282.seq - EST (expressed sequence tag) sequence entries, part 282.
396. gbest283.seq - EST (expressed sequence tag) sequence entries, part 283.
397. gbest284.seq - EST (expressed sequence tag) sequence entries, part 284.
398. gbest285.seq - EST (expressed sequence tag) sequence entries, part 285.
399. gbest286.seq - EST (expressed sequence tag) sequence entries, part 286.
400. gbest287.seq - EST (expressed sequence tag) sequence entries, part 287.
401. gbest288.seq - EST (expressed sequence tag) sequence entries, part 288.
402. gbest289.seq - EST (expressed sequence tag) sequence entries, part 289.
403. gbest290.seq - EST (expressed sequence tag) sequence entries, part 290.
404. gbest291.seq - EST (expressed sequence tag) sequence entries, part 291.
405. gbest292.seq - EST (expressed sequence tag) sequence entries, part 292.
406. gbest293.seq - EST (expressed sequence tag) sequence entries, part 293.
407. gbest294.seq - EST (expressed sequence tag) sequence entries, part 294.
408. gbest295.seq - EST (expressed sequence tag) sequence entries, part 295.
409. gbest296.seq - EST (expressed sequence tag) sequence entries, part 296.
410. gbest297.seq - EST (expressed sequence tag) sequence entries, part 297.
411. gbest298.seq - EST (expressed sequence tag) sequence entries, part 298.
412. gbest299.seq - EST (expressed sequence tag) sequence entries, part 299.
413. gbest300.seq - EST (expressed sequence tag) sequence entries, part 300.
414. gbest301.seq - EST (expressed sequence tag) sequence entries, part 301.
415. gbest302.seq - EST (expressed sequence tag) sequence entries, part 302.
416. gbest303.seq - EST (expressed sequence tag) sequence entries, part 303.
417. gbest304.seq - EST (expressed sequence tag) sequence entries, part 304.
418. gbest305.seq - EST (expressed sequence tag) sequence entries, part 305.
419. gbest306.seq - EST (expressed sequence tag) sequence entries, part 306.
420. gbest307.seq - EST (expressed sequence tag) sequence entries, part 307.
421. gbest308.seq - EST (expressed sequence tag) sequence entries, part 308.
422. gbest309.seq - EST (expressed sequence tag) sequence entries, part 309.
423. gbest310.seq - EST (expressed sequence tag) sequence entries, part 310.
424. gbest311.seq - EST (expressed sequence tag) sequence entries, part 311.
425. gbest312.seq - EST (expressed sequence tag) sequence entries, part 312.
426. gbest313.seq - EST (expressed sequence tag) sequence entries, part 313.
427. gbest314.seq - EST (expressed sequence tag) sequence entries, part 314.
428. gbest315.seq - EST (expressed sequence tag) sequence entries, part 315.
429. gbest316.seq - EST (expressed sequence tag) sequence entries, part 316.
430. gbest317.seq - EST (expressed sequence tag) sequence entries, part 317.
431. gbest318.seq - EST (expressed sequence tag) sequence entries, part 318.
432. gbest319.seq - EST (expressed sequence tag) sequence entries, part 319.
433. gbest320.seq - EST (expressed sequence tag) sequence entries, part 320.
434. gbest321.seq - EST (expressed sequence tag) sequence entries, part 321.
435. gbpat1.seq - Patent sequence entries, part 1.
436. gbpat2.seq - Patent sequence entries, part 2.
437. gbpat3.seq - Patent sequence entries, part 3.
438. gbpat4.seq - Patent sequence entries, part 4.
439. gbpat5.seq - Patent sequence entries, part 5.
440. gbpat6.seq - Patent sequence entries, part 6.
441. gbpat7.seq - Patent sequence entries, part 7.
442. gbpat8.seq - Patent sequence entries, part 8.
443. gbpat9.seq - Patent sequence entries, part 9.
444. gbpat10.seq - Patent sequence entries, part 10.
445. gbpat11.seq - Patent sequence entries, part 11.
446. gbpat12.seq - Patent sequence entries, part 12.
447. gbpat13.seq - Patent sequence entries, part 13.
448. gbpat14.seq - Patent sequence entries, part 14.
449. gbpat15.seq - Patent sequence entries, part 15.
450. gbsts1.seq - STS (sequence tagged site) sequence entries, part 1.
451. gbsts2.seq - STS (sequence tagged site) sequence entries, part 2.
452. gbsts3.seq - STS (sequence tagged site) sequence entries, part 3.
453. gbsts4.seq - STS (sequence tagged site) sequence entries, part 4.
454. gbsts5.seq - STS (sequence tagged site) sequence entries, part 5.
455. gbgss1.seq - GSS (genome survey sequence) sequence entries, part 1.
456. gbgss2.seq - GSS (genome survey sequence) sequence entries, part 2.
457. gbgss3.seq - GSS (genome survey sequence) sequence entries, part 3.
458. gbgss4.seq - GSS (genome survey sequence) sequence entries, part 4.
459. gbgss5.seq - GSS (genome survey sequence) sequence entries, part 5.
460. gbgss6.seq - GSS (genome survey sequence) sequence entries, part 6.
461. gbgss7.seq - GSS (genome survey sequence) sequence entries, part 7.
462. gbgss8.seq - GSS (genome survey sequence) sequence entries, part 8.
463. gbgss9.seq - GSS (genome survey sequence) sequence entries, part 9.
464. gbgss10.seq - GSS (genome survey sequence) sequence entries, part 10.
465. gbgss11.seq - GSS (genome survey sequence) sequence entries, part 11.
466. gbgss12.seq - GSS (genome survey sequence) sequence entries, part 12.
467. gbgss13.seq - GSS (genome survey sequence) sequence entries, part 13.
468. gbgss14.seq - GSS (genome survey sequence) sequence entries, part 14.
469. gbgss15.seq - GSS (genome survey sequence) sequence entries, part 15.
470. gbgss16.seq - GSS (genome survey sequence) sequence entries, part 16.
471. gbgss17.seq - GSS (genome survey sequence) sequence entries, part 17.
472. gbgss18.seq - GSS (genome survey sequence) sequence entries, part 18.
473. gbgss19.seq - GSS (genome survey sequence) sequence entries, part 19.
474. gbgss20.seq - GSS (genome survey sequence) sequence entries, part 20.
475. gbgss21.seq - GSS (genome survey sequence) sequence entries, part 21.
476. gbgss22.seq - GSS (genome survey sequence) sequence entries, part 22.
477. gbgss23.seq - GSS (genome survey sequence) sequence entries, part 23.
478. gbgss24.seq - GSS (genome survey sequence) sequence entries, part 24.
479. gbgss25.seq - GSS (genome survey sequence) sequence entries, part 25.
480. gbgss26.seq - GSS (genome survey sequence) sequence entries, part 26.
481. gbgss27.seq - GSS (genome survey sequence) sequence entries, part 27.
482. gbgss28.seq - GSS (genome survey sequence) sequence entries, part 28.
483. gbgss29.seq - GSS (genome survey sequence) sequence entries, part 29.
484. gbgss30.seq - GSS (genome survey sequence) sequence entries, part 30.
485. gbgss31.seq - GSS (genome survey sequence) sequence entries, part 31.
486. gbgss32.seq - GSS (genome survey sequence) sequence entries, part 32.
487. gbgss33.seq - GSS (genome survey sequence) sequence entries, part 33.
488. gbgss34.seq - GSS (genome survey sequence) sequence entries, part 34.
489. gbgss35.seq - GSS (genome survey sequence) sequence entries, part 35.
490. gbgss36.seq - GSS (genome survey sequence) sequence entries, part 36.
491. gbgss37.seq - GSS (genome survey sequence) sequence entries, part 37.
492. gbgss38.seq - GSS (genome survey sequence) sequence entries, part 38.
493. gbgss39.seq - GSS (genome survey sequence) sequence entries, part 39.
494. gbgss40.seq - GSS (genome survey sequence) sequence entries, part 40.
495. gbgss41.seq - GSS (genome survey sequence) sequence entries, part 41.
496. gbgss42.seq - GSS (genome survey sequence) sequence entries, part 42.
497. gbgss43.seq - GSS (genome survey sequence) sequence entries, part 43.
498. gbgss44.seq - GSS (genome survey sequence) sequence entries, part 44.
499. gbgss45.seq - GSS (genome survey sequence) sequence entries, part 45.
500. gbgss46.seq - GSS (genome survey sequence) sequence entries, part 46.
501. gbgss47.seq - GSS (genome survey sequence) sequence entries, part 47.
502. gbgss48.seq - GSS (genome survey sequence) sequence entries, part 48.
503. gbgss49.seq - GSS (genome survey sequence) sequence entries, part 49.
504. gbgss50.seq - GSS (genome survey sequence) sequence entries, part 50.
505. gbgss51.seq - GSS (genome survey sequence) sequence entries, part 51.
506. gbgss52.seq - GSS (genome survey sequence) sequence entries, part 52.
507. gbgss53.seq - GSS (genome survey sequence) sequence entries, part 53.
508. gbgss54.seq - GSS (genome survey sequence) sequence entries, part 54.
509. gbgss55.seq - GSS (genome survey sequence) sequence entries, part 55.
510. gbgss56.seq - GSS (genome survey sequence) sequence entries, part 56.
511. gbgss57.seq - GSS (genome survey sequence) sequence entries, part 57.
512. gbgss58.seq - GSS (genome survey sequence) sequence entries, part 58.
513. gbgss59.seq - GSS (genome survey sequence) sequence entries, part 59.
514. gbgss60.seq - GSS (genome survey sequence) sequence entries, part 60.
515. gbgss61.seq - GSS (genome survey sequence) sequence entries, part 61.
516. gbgss62.seq - GSS (genome survey sequence) sequence entries, part 62.
517. gbgss63.seq - GSS (genome survey sequence) sequence entries, part 63.
518. gbgss64.seq - GSS (genome survey sequence) sequence entries, part 64.
519. gbgss65.seq - GSS (genome survey sequence) sequence entries, part 65.
520. gbgss66.seq - GSS (genome survey sequence) sequence entries, part 66.
521. gbgss67.seq - GSS (genome survey sequence) sequence entries, part 67.
522. gbgss68.seq - GSS (genome survey sequence) sequence entries, part 68.
523. gbgss69.seq - GSS (genome survey sequence) sequence entries, part 69.
524. gbgss70.seq - GSS (genome survey sequence) sequence entries, part 70.
525. gbgss71.seq - GSS (genome survey sequence) sequence entries, part 71.
526. gbgss72.seq - GSS (genome survey sequence) sequence entries, part 72.
527. gbgss73.seq - GSS (genome survey sequence) sequence entries, part 73.
528. gbgss74.seq - GSS (genome survey sequence) sequence entries, part 74.
529. gbgss75.seq - GSS (genome survey sequence) sequence entries, part 75.
530. gbgss76.seq - GSS (genome survey sequence) sequence entries, part 76.
531. gbgss77.seq - GSS (genome survey sequence) sequence entries, part 77.
532. gbgss78.seq - GSS (genome survey sequence) sequence entries, part 78.
533. gbgss79.seq - GSS (genome survey sequence) sequence entries, part 79.
534. gbgss80.seq - GSS (genome survey sequence) sequence entries, part 80.
535. gbgss81.seq - GSS (genome survey sequence) sequence entries, part 81.
536. gbgss82.seq - GSS (genome survey sequence) sequence entries, part 82.
537. gbgss83.seq - GSS (genome survey sequence) sequence entries, part 83.
538. gbgss84.seq - GSS (genome survey sequence) sequence entries, part 84.
539. gbgss85.seq - GSS (genome survey sequence) sequence entries, part 85.
540. gbgss86.seq - GSS (genome survey sequence) sequence entries, part 86.
541. gbgss87.seq - GSS (genome survey sequence) sequence entries, part 87.
542. gbgss88.seq - GSS (genome survey sequence) sequence entries, part 88.
543. gbgss89.seq - GSS (genome survey sequence) sequence entries, part 89.
544. gbgss90.seq - GSS (genome survey sequence) sequence entries, part 90.
545. gbgss91.seq - GSS (genome survey sequence) sequence entries, part 91.
546. gbgss92.seq - GSS (genome survey sequence) sequence entries, part 92.
547. gbgss93.seq - GSS (genome survey sequence) sequence entries, part 93.
548. gbgss94.seq - GSS (genome survey sequence) sequence entries, part 94.
549. gbgss95.seq - GSS (genome survey sequence) sequence entries, part 95.
550. gbgss96.seq - GSS (genome survey sequence) sequence entries, part 96.
551. gbgss97.seq - GSS (genome survey sequence) sequence entries, part 97.
552. gbgss98.seq - GSS (genome survey sequence) sequence entries, part 98.
553. gbgss99.seq - GSS (genome survey sequence) sequence entries, part 99.
554. gbgss100.seq - GSS (genome survey sequence) sequence entries, part 100.
555. gbgss101.seq - GSS (genome survey sequence) sequence entries, part 101.
556. gbgss102.seq - GSS (genome survey sequence) sequence entries, part 102.
557. gbgss103.seq - GSS (genome survey sequence) sequence entries, part 103.
558. gbgss104.seq - GSS (genome survey sequence) sequence entries, part 104.
559. gbgss105.seq - GSS (genome survey sequence) sequence entries, part 105.
560. gbgss106.seq - GSS (genome survey sequence) sequence entries, part 106.
561. gbgss107.seq - GSS (genome survey sequence) sequence entries, part 107.
562. gbgss108.seq - GSS (genome survey sequence) sequence entries, part 108.
563. gbgss109.seq - GSS (genome survey sequence) sequence entries, part 109.
564. gbgss110.seq - GSS (genome survey sequence) sequence entries, part 110.
565. gbhtg1.seq - HTGS (high throughput genomic sequencing) sequence entries, part 1.
566. gbhtg2.seq - HTGS (high throughput genomic sequencing) sequence entries, part 2.
567. gbhtg3.seq - HTGS (high throughput genomic sequencing) sequence entries, part 3.
568. gbhtg4.seq - HTGS (high throughput genomic sequencing) sequence entries, part 4.
569. gbhtg5.seq - HTGS (high throughput genomic sequencing) sequence entries, part 5.
570. gbhtg6.seq - HTGS (high throughput genomic sequencing) sequence entries, part 6.
571. gbhtg7.seq - HTGS (high throughput genomic sequencing) sequence entries, part 7.
572. gbhtg8.seq - HTGS (high throughput genomic sequencing) sequence entries, part 8.
573. gbhtg9.seq - HTGS (high throughput genomic sequencing) sequence entries, part 9.
574. gbhtg10.seq - HTGS (high throughput genomic sequencing) sequence entries, part 10.
575. gbhtg11.seq - HTGS (high throughput genomic sequencing) sequence entries, part 11.
576. gbhtg12.seq - HTGS (high throughput genomic sequencing) sequence entries, part 12.
577. gbhtg13.seq - HTGS (high throughput genomic sequencing) sequence entries, part 13.
578. gbhtg14.seq - HTGS (high throughput genomic sequencing) sequence entries, part 14.
579. gbhtg15.seq - HTGS (high throughput genomic sequencing) sequence entries, part 15.
580. gbhtg16.seq - HTGS (high throughput genomic sequencing) sequence entries, part 16.
581. gbhtg17.seq - HTGS (high throughput genomic sequencing) sequence entries, part 17.
582. gbhtg18.seq - HTGS (high throughput genomic sequencing) sequence entries, part 18.
583. gbhtg19.seq - HTGS (high throughput genomic sequencing) sequence entries, part 19.
584. gbhtg20.seq - HTGS (high throughput genomic sequencing) sequence entries, part 20.
585. gbhtg21.seq - HTGS (high throughput genomic sequencing) sequence entries, part 21.
586. gbhtg22.seq - HTGS (high throughput genomic sequencing) sequence entries, part 22.
587. gbhtg23.seq - HTGS (high throughput genomic sequencing) sequence entries, part 23.
588. gbhtg24.seq - HTGS (high throughput genomic sequencing) sequence entries, part 24.
589. gbhtg25.seq - HTGS (high throughput genomic sequencing) sequence entries, part 25.
590. gbhtg26.seq - HTGS (high throughput genomic sequencing) sequence entries, part 26.
591. gbhtg27.seq - HTGS (high throughput genomic sequencing) sequence entries, part 27.
592. gbhtg28.seq - HTGS (high throughput genomic sequencing) sequence entries, part 28.
593. gbhtg29.seq - HTGS (high throughput genomic sequencing) sequence entries, part 29.
594. gbhtg30.seq - HTGS (high throughput genomic sequencing) sequence entries, part 30.
595. gbhtg31.seq - HTGS (high throughput genomic sequencing) sequence entries, part 31.
596. gbhtg32.seq - HTGS (high throughput genomic sequencing) sequence entries, part 32.
597. gbhtg33.seq - HTGS (high throughput genomic sequencing) sequence entries, part 33.
598. gbhtg34.seq - HTGS (high throughput genomic sequencing) sequence entries, part 34.
599. gbhtg35.seq - HTGS (high throughput genomic sequencing) sequence entries, part 35.
600. gbhtg36.seq - HTGS (high throughput genomic sequencing) sequence entries, part 36.
601. gbhtg37.seq - HTGS (high throughput genomic sequencing) sequence entries, part 37.
602. gbhtg38.seq - HTGS (high throughput genomic sequencing) sequence entries, part 38.
603. gbhtg39.seq - HTGS (high throughput genomic sequencing) sequence entries, part 39.
604. gbhtg40.seq - HTGS (high throughput genomic sequencing) sequence entries, part 40.
605. gbhtg41.seq - HTGS (high throughput genomic sequencing) sequence entries, part 41.
606. gbhtg42.seq - HTGS (high throughput genomic sequencing) sequence entries, part 42.
607. gbhtg43.seq - HTGS (high throughput genomic sequencing) sequence entries, part 43.
608. gbhtg44.seq - HTGS (high throughput genomic sequencing) sequence entries, part 44.
609. gbhtg45.seq - HTGS (high throughput genomic sequencing) sequence entries, part 45.
610. gbhtg46.seq - HTGS (high throughput genomic sequencing) sequence entries, part 46.
611. gbhtg47.seq - HTGS (high throughput genomic sequencing) sequence entries, part 47.
612. gbhtg48.seq - HTGS (high throughput genomic sequencing) sequence entries, part 48.
613. gbhtg49.seq - HTGS (high throughput genomic sequencing) sequence entries, part 49.
614. gbhtg50.seq - HTGS (high throughput genomic sequencing) sequence entries, part 50.
615. gbhtg51.seq - HTGS (high throughput genomic sequencing) sequence entries, part 51.
616. gbhtg52.seq - HTGS (high throughput genomic sequencing) sequence entries, part 52.
617. gbhtg53.seq - HTGS (high throughput genomic sequencing) sequence entries, part 53.
618. gbhtg54.seq - HTGS (high throughput genomic sequencing) sequence entries, part 54.
619. gbhtg55.seq - HTGS (high throughput genomic sequencing) sequence entries, part 55.
620. gbhtg56.seq - HTGS (high throughput genomic sequencing) sequence entries, part 56.
621. gbhtg57.seq - HTGS (high throughput genomic sequencing) sequence entries, part 57.
622. gbhtg58.seq - HTGS (high throughput genomic sequencing) sequence entries, part 58.
623. gbhtg59.seq - HTGS (high throughput genomic sequencing) sequence entries, part 59.
624. gbhtg60.seq - HTGS (high throughput genomic sequencing) sequence entries, part 60.
625. gbhtg61.seq - HTGS (high throughput genomic sequencing) sequence entries, part 61.
626. gbhtg62.seq - HTGS (high throughput genomic sequencing) sequence entries, part 62.
627. gbhtc1.seq - HTC (high throughput cDNA sequencing) entries, part 1.
628. gbhtc2.seq - HTC (high throughput cDNA sequencing) entries, part 2.
629. gbhtc3.seq - HTC (high throughput cDNA sequencing) entries, part 3.
630. gbhtc4.seq - HTC (high throughput cDNA sequencing) entries, part 4.
631. gbcon.seq - CON division entries (see description below for details)
632. gbchg.txt - Accession numbers of entries updated since the previous release.
633. gbdel.txt - Accession numbers of entries deleted since the previous release.
634. gbnew.txt - Accession numbers of entries new since the previous release.
The gbcon.seq data file provides an alternative representation for complex
sequences, such as segmented sets and complete-genomes that have been split
into pieces. These "CON" records do not contain sequence data; they utilize
a CONTIG linetype with a join() statement which describes how the component
sequences can be assembled to form the larger sequence. The contents of the
CON division are not reflected in the 'index', 'new', 'chg', and 'del' files
that accompany GenBank releases, nor in release statistics (Sections 2.2.6,
2.2.7, and 2.2.8). The GenBank README describes the CON division of GenBank
in more detail:
ftp://ftp.ncbi.nih.gov/genbank/README.genbank
2.2.5 File Sizes
Uncompressed, the Release 142.0 flatfiles require roughly 136 GB (sequence
files only) or 153 GB (including the 'short directory', 'index' and the
*.txt files). The following table contains the approximate sizes of the
individual files in this release. Since minor changes to some of the files
might have occurred after these release notes were written, these sizes should
not be used to determine file integrity; they are provided as an aid to
planning only.
File Size File Name
1094092495 gbacc.idx
501001237 gbaut1.idx
501269250 gbaut10.idx
510199443 gbaut11.idx
500172574 gbaut12.idx
500272312 gbaut13.idx
502226804 gbaut14.idx
512574018 gbaut15.idx
500099644 gbaut16.idx
505899947 gbaut17.idx
506994062 gbaut18.idx
501961608 gbaut19.idx
500366986 gbaut2.idx
508420926 gbaut20.idx
500282002 gbaut21.idx
500314031 gbaut22.idx
500058497 gbaut23.idx
517457852 gbaut24.idx
26317729 gbaut25.idx
516628529 gbaut3.idx
501146250 gbaut4.idx
519082231 gbaut5.idx
501134349 gbaut6.idx
507054654 gbaut7.idx
502369999 gbaut8.idx
507059458 gbaut9.idx
250017376 gbbct1.seq
250004302 gbbct2.seq
250138105 gbbct3.seq
249993816 gbbct4.seq
250299993 gbbct5.seq
250009967 gbbct6.seq
250570017 gbbct7.seq
249892692 gbbct8.seq
141196800 gbbct9.seq
5347988 gbchg.txt
498807178 gbcon.seq
65134 gbdel.txt
230689132 gbest1.seq
230688600 gbest10.seq
230689508 gbest100.seq
230688230 gbest101.seq
230688169 gbest102.seq
230688583 gbest103.seq
230690105 gbest104.seq
230687989 gbest105.seq
230690404 gbest106.seq
230605896 gbest107.seq
230687451 gbest108.seq
230689026 gbest109.seq
230689016 gbest11.seq
230687990 gbest110.seq
230688227 gbest111.seq
230688521 gbest112.seq
230687496 gbest113.seq
230688937 gbest114.seq
230687701 gbest115.seq
230689445 gbest116.seq
230688034 gbest117.seq
230690334 gbest118.seq
230690331 gbest119.seq
230688477 gbest12.seq
230688842 gbest120.seq
230688435 gbest121.seq
230689502 gbest122.seq
230690248 gbest123.seq
230689256 gbest124.seq
230689775 gbest125.seq
230688637 gbest126.seq
230689208 gbest127.seq
230690090 gbest128.seq
230689951 gbest129.seq
230689137 gbest13.seq
230688344 gbest130.seq
230688046 gbest131.seq
230688094 gbest132.seq
230690467 gbest133.seq
230687956 gbest134.seq
230690441 gbest135.seq
230688581 gbest136.seq
230689108 gbest137.seq
230688708 gbest138.seq
230688243 gbest139.seq
230689634 gbest14.seq
230687498 gbest140.seq
230687508 gbest141.seq
230688181 gbest142.seq
230688663 gbest143.seq
230688759 gbest144.seq
230691126 gbest145.seq
230690387 gbest146.seq
230687443 gbest147.seq
230687541 gbest148.seq
230690200 gbest149.seq
230690083 gbest15.seq
230689750 gbest150.seq
230690297 gbest151.seq
230690005 gbest152.seq
230689822 gbest153.seq
230688829 gbest154.seq
230688960 gbest155.seq
230688107 gbest156.seq
230690388 gbest157.seq
230690222 gbest158.seq
230690726 gbest159.seq
230688068 gbest16.seq
230688850 gbest160.seq
230689625 gbest161.seq
230687848 gbest162.seq
230691396 gbest163.seq
230689445 gbest164.seq
230687445 gbest165.seq
230689599 gbest166.seq
230310104 gbest167.seq
230689946 gbest168.seq
230688910 gbest169.seq
230689621 gbest17.seq
230691086 gbest170.seq
230689084 gbest171.seq
230689167 gbest172.seq
230689215 gbest173.seq
230689822 gbest174.seq
230690314 gbest175.seq
230690186 gbest176.seq
230690844 gbest177.seq
230687906 gbest178.seq
230688796 gbest179.seq
230689802 gbest18.seq
230690375 gbest180.seq
230689388 gbest181.seq
230688720 gbest182.seq
230689464 gbest183.seq
230689588 gbest184.seq
230688916 gbest185.seq
230688557 gbest186.seq
230688541 gbest187.seq
230691568 gbest188.seq
230690509 gbest189.seq
230688799 gbest19.seq
230690568 gbest190.seq
230688390 gbest191.seq
230688922 gbest192.seq
230688033 gbest193.seq
230689008 gbest194.seq
230688707 gbest195.seq
230688270 gbest196.seq
230688865 gbest197.seq
230688899 gbest198.seq
230689754 gbest199.seq
230689481 gbest2.seq
230688740 gbest20.seq
230689851 gbest200.seq
230690470 gbest201.seq
230690505 gbest202.seq
230692917 gbest203.seq
165721583 gbest204.seq
162548168 gbest205.seq
166146854 gbest206.seq
170129660 gbest207.seq
169829644 gbest208.seq
164118786 gbest209.seq
230689731 gbest21.seq
165255453 gbest210.seq
164665005 gbest211.seq
164462331 gbest212.seq
164681420 gbest213.seq
164380276 gbest214.seq
164136086 gbest215.seq
163661500 gbest216.seq
167949127 gbest217.seq
162119867 gbest218.seq
164068475 gbest219.seq
230688256 gbest22.seq
168545161 gbest220.seq
167261132 gbest221.seq
165946168 gbest222.seq
165858864 gbest223.seq
165520033 gbest224.seq
165269500 gbest225.seq
164388930 gbest226.seq
164456575 gbest227.seq
165609330 gbest228.seq
167741649 gbest229.seq
230688401 gbest23.seq
180424960 gbest230.seq
170956131 gbest231.seq
204351582 gbest232.seq
230689411 gbest233.seq
230688335 gbest234.seq
230687498 gbest235.seq
230687516 gbest236.seq
230689873 gbest237.seq
230687469 gbest238.seq
230687739 gbest239.seq
230688396 gbest24.seq
230691157 gbest240.seq
230687811 gbest241.seq
230688114 gbest242.seq
230687913 gbest243.seq
230688434 gbest244.seq
230690014 gbest245.seq
230689379 gbest246.seq
230689358 gbest247.seq
230689443 gbest248.seq
230687674 gbest249.seq
230689347 gbest25.seq
230690233 gbest250.seq
230688741 gbest251.seq
230689725 gbest252.seq
230690808 gbest253.seq
230687605 gbest254.seq
230689671 gbest255.seq
230687806 gbest256.seq
230688617 gbest257.seq
230690960 gbest258.seq
230687844 gbest259.seq
230690653 gbest26.seq
230690297 gbest260.seq
207754938 gbest261.seq
230690912 gbest262.seq
230689980 gbest263.seq
230688470 gbest264.seq
230689994 gbest265.seq
230689077 gbest266.seq
230689488 gbest267.seq
230690693 gbest268.seq
230687904 gbest269.seq
230688555 gbest27.seq
230687898 gbest270.seq
230688642 gbest271.seq
230689861 gbest272.seq
230691236 gbest273.seq
230687811 gbest274.seq
230689115 gbest275.seq
230688202 gbest276.seq
230687859 gbest277.seq
230688347 gbest278.seq
230687885 gbest279.seq
230689082 gbest28.seq
230687632 gbest280.seq
230689234 gbest281.seq
230687566 gbest282.seq
230687867 gbest283.seq
230689571 gbest284.seq
230687659 gbest285.seq
230690375 gbest286.seq
230690417 gbest287.seq
230691112 gbest288.seq
230690875 gbest289.seq
230689872 gbest29.seq
222137184 gbest290.seq
155805792 gbest291.seq
230690249 gbest292.seq
230689954 gbest293.seq
230688453 gbest294.seq
230689863 gbest295.seq
230689333 gbest296.seq
230689862 gbest297.seq
230689744 gbest298.seq
230689230 gbest299.seq
230689555 gbest3.seq
230688133 gbest30.seq
230688871 gbest300.seq
230689684 gbest301.seq
230688783 gbest302.seq
230692219 gbest303.seq
230687986 gbest304.seq
230689994 gbest305.seq
230692265 gbest306.seq
230690444 gbest307.seq
230689530 gbest308.seq
230689758 gbest309.seq
230689058 gbest31.seq
230688449 gbest310.seq
230688681 gbest311.seq
230687934 gbest312.seq
230689966 gbest313.seq
230688201 gbest314.seq
230687646 gbest315.seq
230687614 gbest316.seq
230690141 gbest317.seq
223524739 gbest318.seq
230687727 gbest319.seq
230688406 gbest32.seq
230687517 gbest320.seq
19933519 gbest321.seq
230688288 gbest33.seq
230689866 gbest34.seq
230688478 gbest35.seq
229366503 gbest36.seq
191408157 gbest37.seq
190329541 gbest38.seq
213443983 gbest39.seq
230687893 gbest4.seq
216071978 gbest40.seq
215846261 gbest41.seq
216894887 gbest42.seq
230688911 gbest43.seq
230687461 gbest44.seq
227369696 gbest45.seq
230387383 gbest46.seq
230688991 gbest47.seq
230688082 gbest48.seq
230688687 gbest49.seq
163953101 gbest5.seq
230688411 gbest50.seq
230689704 gbest51.seq
230688163 gbest52.seq
230688349 gbest53.seq
230689694 gbest54.seq
230688785 gbest55.seq
230689520 gbest56.seq
230687609 gbest57.seq
230690396 gbest58.seq
230689241 gbest59.seq
180514745 gbest6.seq
230688642 gbest60.seq
230691917 gbest61.seq
209702259 gbest62.seq
209361834 gbest63.seq
208354185 gbest64.seq
209103080 gbest65.seq
209842385 gbest66.seq
210140845 gbest67.seq
209461780 gbest68.seq
208459913 gbest69.seq
230687546 gbest7.seq
210134383 gbest70.seq
208147495 gbest71.seq
205313146 gbest72.seq
208393023 gbest73.seq
208080020 gbest74.seq
211617124 gbest75.seq
226038921 gbest76.seq
230689369 gbest77.seq
230689369 gbest78.seq
221510648 gbest79.seq
230689300 gbest8.seq
214455847 gbest80.seq
213859355 gbest81.seq
230689222 gbest82.seq
230689172 gbest83.seq
230687931 gbest84.seq
230688477 gbest85.seq
230689029 gbest86.seq
230689104 gbest87.seq
230687540 gbest88.seq
230688232 gbest89.seq
230687459 gbest9.seq
230689961 gbest90.seq
230687820 gbest91.seq
230688921 gbest92.seq
230688071 gbest93.seq
230690244 gbest94.seq
230687464 gbest95.seq
230690342 gbest96.seq
230687524 gbest97.seq
230689371 gbest98.seq
230689348 gbest99.seq
37415391 gbgen.idx
230688486 gbgss1.seq
230688594 gbgss10.seq
250002289 gbgss100.seq
250001805 gbgss101.seq
250001572 gbgss102.seq
250002854 gbgss103.seq
250002040 gbgss104.seq
250001553 gbgss105.seq
250003640 gbgss106.seq
250002221 gbgss107.seq
250000702 gbgss108.seq
250002184 gbgss109.seq
230690231 gbgss11.seq
112108641 gbgss110.seq
230688049 gbgss12.seq
230689543 gbgss13.seq
230690171 gbgss14.seq
230688245 gbgss15.seq
230690296 gbgss16.seq
230687640 gbgss17.seq
230687827 gbgss18.seq
230688676 gbgss19.seq
230687986 gbgss2.seq
230689023 gbgss20.seq
230690916 gbgss21.seq
230690080 gbgss22.seq
230689158 gbgss23.seq
230688311 gbgss24.seq
230689375 gbgss25.seq
230687576 gbgss26.seq
230687630 gbgss27.seq
230688320 gbgss28.seq
230687705 gbgss29.seq
230687901 gbgss3.seq
230690534 gbgss30.seq
230688179 gbgss31.seq
230688390 gbgss32.seq
230688360 gbgss33.seq
230688142 gbgss34.seq
230688663 gbgss35.seq
230688387 gbgss36.seq
230687494 gbgss37.seq
230689000 gbgss38.seq
230689610 gbgss39.seq
230687845 gbgss4.seq
230689557 gbgss40.seq
230689813 gbgss41.seq
230687530 gbgss42.seq
230689127 gbgss43.seq
230687738 gbgss44.seq
230688290 gbgss45.seq
230688229 gbgss46.seq
230688412 gbgss47.seq
230687615 gbgss48.seq
230688420 gbgss49.seq
230687801 gbgss5.seq
230688773 gbgss50.seq
230687676 gbgss51.seq
230688817 gbgss52.seq
230687699 gbgss53.seq
230689919 gbgss54.seq
230688862 gbgss55.seq
230690237 gbgss56.seq
230687775 gbgss57.seq
230688980 gbgss58.seq
230687649 gbgss59.seq
230690143 gbgss6.seq
230688258 gbgss60.seq
230148833 gbgss61.seq
230689960 gbgss62.seq
230690155 gbgss63.seq
230687478 gbgss64.seq
230688521 gbgss65.seq
230687908 gbgss66.seq
230688422 gbgss67.seq
230689430 gbgss68.seq
230688820 gbgss69.seq
230687660 gbgss7.seq
230688221 gbgss70.seq
230687661 gbgss71.seq
230688972 gbgss72.seq
230688503 gbgss73.seq
230689378 gbgss74.seq
230689620 gbgss75.seq
230687774 gbgss76.seq
230689151 gbgss77.seq
230689335 gbgss78.seq
230687776 gbgss79.seq
230690622 gbgss8.seq
205544344 gbgss80.seq
193687138 gbgss81.seq
213364532 gbgss82.seq
230689093 gbgss83.seq
230687888 gbgss84.seq
230687956 gbgss85.seq
230689410 gbgss86.seq
230688582 gbgss87.seq
230688819 gbgss88.seq
230688637 gbgss89.seq
230689742 gbgss9.seq
230689731 gbgss90.seq
230687942 gbgss91.seq
160278782 gbgss92.seq
250000689 gbgss93.seq
250002709 gbgss94.seq
250002244 gbgss95.seq
250000255 gbgss96.seq
250000195 gbgss97.seq
250001730 gbgss98.seq
250001987 gbgss99.seq
250000146 gbhtc1.seq
250002208 gbhtc2.seq
250001806 gbhtc3.seq
89344059 gbhtc4.seq
250045190 gbhtg1.seq
250050766 gbhtg10.seq
250204523 gbhtg11.seq
250171440 gbhtg12.seq
250318070 gbhtg13.seq
250108487 gbhtg14.seq
250524986 gbhtg15.seq
250214068 gbhtg16.seq
250118614 gbhtg17.seq
250072292 gbhtg18.seq
250012711 gbhtg19.seq
250075466 gbhtg2.seq
250121357 gbhtg20.seq
250213041 gbhtg21.seq
250111291 gbhtg22.seq
250146361 gbhtg23.seq
250451259 gbhtg24.seq
250133253 gbhtg25.seq
250064311 gbhtg26.seq
250209816 gbhtg27.seq
250156750 gbhtg28.seq
250301811 gbhtg29.seq
250115515 gbhtg3.seq
250196353 gbhtg30.seq
250262638 gbhtg31.seq
250173828 gbhtg32.seq
250118085 gbhtg33.seq
250372564 gbhtg34.seq
250301641 gbhtg35.seq
250300186 gbhtg36.seq
250034570 gbhtg37.seq
250247371 gbhtg38.seq
250260620 gbhtg39.seq
250226246 gbhtg4.seq
250117571 gbhtg40.seq
250055788 gbhtg41.seq
250187466 gbhtg42.seq
250057271 gbhtg43.seq
250112389 gbhtg44.seq
250198417 gbhtg45.seq
250209150 gbhtg46.seq
250112543 gbhtg47.seq
250026448 gbhtg48.seq
250178056 gbhtg49.seq
250021518 gbhtg5.seq
250212931 gbhtg50.seq
250159403 gbhtg51.seq
250205391 gbhtg52.seq
250026031 gbhtg53.seq
250167100 gbhtg54.seq
250085309 gbhtg55.seq
250019348 gbhtg56.seq
250169626 gbhtg57.seq
250157540 gbhtg58.seq
250257515 gbhtg59.seq
250175997 gbhtg6.seq
250195607 gbhtg60.seq
250490410 gbhtg61.seq
11869772 gbhtg62.seq
250139646 gbhtg7.seq
250179681 gbhtg8.seq
250042907 gbhtg9.seq
250125341 gbinv1.seq
250036227 gbinv2.seq
250003257 gbinv3.seq
250000384 gbinv4.seq
249993904 gbinv5.seq
214049706 gbinv6.seq
777780721 gbkey.idx
221854715 gbmam.seq
29047550 gbnew.txt
250023974 gbpat1.seq
250001045 gbpat10.seq
250000131 gbpat11.seq
250005834 gbpat12.seq
250000365 gbpat13.seq
250000566 gbpat14.seq
159229150 gbpat15.seq
250000547 gbpat2.seq
250000874 gbpat3.seq
250000949 gbpat4.seq
250014316 gbpat5.seq
250000552 gbpat6.seq
250000904 gbpat7.seq
250000946 gbpat8.seq
250003388 gbpat9.seq
32266864 gbphg.seq
250083859 gbpln1.seq
250012538 gbpln10.seq
249968998 gbpln11.seq
5479491 gbpln12.seq
250226453 gbpln2.seq
249971308 gbpln3.seq
250003276 gbpln4.seq
250138108 gbpln5.seq
250140855 gbpln6.seq
250001362 gbpln7.seq
250000106 gbpln8.seq
250110106 gbpln9.seq
250253323 gbpri1.seq
250165256 gbpri10.seq
250075024 gbpri11.seq
250073507 gbpri12.seq
250203677 gbpri13.seq
250105912 gbpri14.seq
250002127 gbpri15.seq
250000747 gbpri16.seq
250054068 gbpri17.seq
250181133 gbpri18.seq
250095112 gbpri19.seq
250065713 gbpri2.seq
250010745 gbpri20.seq
250191965 gbpri21.seq
250004376 gbpri22.seq
250026252 gbpri23.seq
250097348 gbpri24.seq
250000052 gbpri25.seq
250004642 gbpri26.seq
249989039 gbpri27.seq
13058933 gbpri28.seq
250144057 gbpri3.seq
250190447 gbpri4.seq
250142335 gbpri5.seq
250062313 gbpri6.seq
250074178 gbpri7.seq
250192144 gbpri8.seq
250040773 gbpri9.seq
170050 gbrel.txt
250230902 gbrod1.seq
250067333 gbrod10.seq
250002703 gbrod11.seq
250047193 gbrod12.seq
34770711 gbrod13.seq
250212397 gbrod2.seq
250060400 gbrod3.seq
250168063 gbrod4.seq
250043947 gbrod5.seq
250077297 gbrod6.seq
250000208 gbrod7.seq
250087506 gbrod8.seq
250035669 gbrod9.seq
1528991 gbsec.idx
250001551 gbsts1.seq
250003453 gbsts2.seq
250002286 gbsts3.seq
250001265 gbsts4.seq
59467482 gbsts5.seq
52036837 gbsyn.seq
3047781 gbuna.seq
249999626 gbvrl1.seq
249931363 gbvrl2.seq
249955085 gbvrl3.seq
55837104 gbvrl4.seq
249991963 gbvrt1.seq
250002203 gbvrt2.seq
225560132 gbvrt3.seq
250031401 gbvrt4.seq
250016774 gbvrt5.seq
192754946 gbvrt6.seq
2.2.6 Per-Division Statistics
The following table provides a per-division breakdown of the number of
sequence entries and the total number of bases of DNA/RNA in each non-WGS
sequence data file:
Division Entries Bases
BCT1 28788 98084426
BCT2 8692 106067300
BCT3 397 114375595
BCT4 59594 89611609
BCT5 15749 106192310
BCT6 54776 91559251
BCT7 25545 93326963
BCT8 36017 96145118
BCT9 24249 49924099
EST1 68591 26476165
EST10 76948 29968463
EST100 72829 33437629
EST101 69803 29578910
EST102 67406 38244971
EST103 68738 36302932
EST104 68670 43031045
EST105 73435 35199873
EST106 75673 34898189
EST107 75092 27423511
EST108 74239 35925887
EST109 74255 34795797
EST11 76417 28993121
EST110 66842 39647310
EST111 81394 44491935
EST112 77737 45616051
EST113 69965 45512580
EST114 66965 41738814
EST115 75033 50416014
EST116 69971 42572618
EST117 75984 44762576
EST118 74327 46638700
EST119 72259 47883801
EST12 77097 30819336
EST120 74056 51219887
EST121 79311 40043979
EST122 76489 31066903
EST123 79433 40387867
EST124 78018 42671050
EST125 77038 47622266
EST126 61046 28140606
EST127 72620 38953051
EST128 68100 39977840
EST129 66931 36088071
EST13 77755 29954812
EST130 71760 43925751
EST131 73262 44642166
EST132 68033 39377845
EST133 73310 42015045
EST134 70553 43069101
EST135 62839 39400040
EST136 78358 42436746
EST137 99464 54719272
EST138 66773 36883050
EST139 104576 55177669
EST14 80007 32112984
EST140 110285 58782183
EST141 100664 55991292
EST142 81754 48099109
EST143 91942 52648583
EST144 98730 60770051
EST145 72631 42808454
EST146 65225 31724386
EST147 64108 29199844
EST148 53839 25445070
EST149 66691 32424134
EST15 73059 30970804
EST150 57960 29405699
EST151 73154 43390072
EST152 69437 45357436
EST153 70542 49643310
EST154 77056 44155607
EST155 58985 30334007
EST156 65406 33848312
EST157 66702 38364309
EST158 64443 45716741
EST159 63074 36169422
EST16 75614 33241540
EST160 100422 46238660
EST161 89897 52238199
EST162 84692 48443008
EST163 64754 45673009
EST164 70559 36854528
EST165 57041 32681386
EST166 70929 45158839
EST167 73298 27487470
EST168 76671 43677902
EST169 74209 38791253
EST17 84024 34384350
EST170 69095 35221325
EST171 68611 39105296
EST172 70686 52921474
EST173 68963 40568954
EST174 68682 34570371
EST175 69967 53002280
EST176 68881 47070260
EST177 72896 37403543
EST178 68630 46335520
EST179 70836 58844474
EST18 80464 32530977
EST180 64282 47740025
EST181 64033 46972359
EST182 64318 46429661
EST183 65261 46273746
EST184 67790 51562629
EST185 62429 39577642
EST186 63718 35932610
EST187 64090 36787522
EST188 70161 40145938
EST189 92706 51558487
EST19 81044 33619111
EST190 69052 49401485
EST191 92130 54735395
EST192 106991 66190609
EST193 108657 64465793
EST194 107856 64997801
EST195 103074 67027080
EST196 77921 45028818
EST197 70186 44538833
EST198 69970 59611748
EST199 74355 55489866
EST2 75366 28937064
EST20 72961 29221409
EST200 78109 39860994
EST201 80754 48544402
EST202 73086 52412251
EST203 74304 48345092
EST204 27455 10165197
EST205 27882 10595334
EST206 27294 10130934
EST207 26608 9688585
EST208 26731 9068628
EST209 27599 10053234
EST21 73196 34162066
EST210 27260 9838027
EST211 27285 9884554
EST212 27319 10895071
EST213 27206 11848529
EST214 27285 11083028
EST215 27476 9811863
EST216 27607 9137520
EST217 27037 9902760
EST218 27942 11143045
EST219 27673 11058954
EST22 76944 30614408
EST220 26876 11348378
EST221 26800 12178137
EST222 27167 10983393
EST223 27085 11004986
EST224 27095 11955162
EST225 27253 11473448
EST226 27332 10803070
EST227 27318 10918404
EST228 27190 10382696
EST229 26793 12826151
EST23 77267 32135581
EST230 24553 17169378
EST231 26071 17518439
EST232 69457 25817678
EST233 96909 41276912
EST234 74074 46017028
EST235 70138 45103535
EST236 70002 44866054
EST237 69408 42978490
EST238 77370 44891796
EST239 66282 40886763
EST24 75827 34288929
EST240 71487 49307451
EST241 56357 27429103
EST242 99336 47319968
EST243 91074 45325414
EST244 71738 40068897
EST245 62304 29135275
EST246 70511 45381095
EST247 72337 35523087
EST248 72393 34226209
EST249 70693 43968460
EST25 72604 30893576
EST250 69995 37831883
EST251 66201 39275655
EST252 74512 36299726
EST253 86880 48298809
EST254 78016 52897895
EST255 80808 56334065
EST256 110651 49789456
EST257 86678 44292241
EST258 74392 45235362
EST259 73836 40921856
EST26 76648 31598546
EST260 72878 38649878
EST261 69702 27469528
EST262 70613 41642459
EST263 62529 34148284
EST264 66430 43108110
EST265 71887 40932482
EST266 63526 44703687
EST267 64169 32193693
EST268 82736 43937416
EST269 83931 45417326
EST27 78604 34593850
EST270 93770 53309572
EST271 116550 49714985
EST272 101149 44550714
EST273 66663 36216924
EST274 70129 41169608
EST275 77875 45264282
EST276 76028 38756953
EST277 71525 45663414
EST278 70013 37679621
EST279 61924 37735006
EST28 107725 52346911
EST280 49116 25828533
EST281 63795 40367066
EST282 66967 41420714
EST283 72765 41976284
EST284 69292 40481705
EST285 75809 45585072
EST286 61071 52646504
EST287 63611 48126693
EST288 63086 38623589
EST289 67317 41804396
EST29 71527 43460161
EST290 72637 45792218
EST291 58009 28772411
EST292 68596 36597740
EST293 60475 34042198
EST294 64203 32602663
EST295 62234 39343187
EST296 84837 42917488
EST297 71390 42313222
EST298 69176 44149118
EST299 65112 37461554
EST3 74213 30128080
EST30 72069 58602224
EST300 69333 45386075
EST301 93701 52304549
EST302 87284 51889163
EST303 71622 38701796
EST304 57110 36585307
EST305 77226 38203958
EST306 52877 29016969
EST307 54570 29095703
EST308 72065 43579228
EST309 98852 45887516
EST31 85698 49008414
EST310 74798 45919016
EST311 74930 49940139
EST312 80802 52790427
EST313 100535 43899175
EST314 75837 26100856
EST315 72585 26563538
EST316 74175 26642878
EST317 73540 26877579
EST318 78213 26074037
EST319 72795 28973891
EST32 84274 43170200
EST320 73315 28517243
EST321 7656 2416414
EST33 93780 46027156
EST34 100230 48158543
EST35 99471 50721448
EST36 96874 38305090
EST37 69226 18544233
EST38 69423 18463478
EST39 65282 20003105
EST4 74631 28188475
EST40 43582 11803972
EST41 43296 12056612
EST42 43090 11431891
EST43 72759 28458352
EST44 96291 44422472
EST45 93572 46244075
EST46 90620 43419833
EST47 101758 51479957
EST48 102258 52220140
EST49 76413 33051064
EST5 48531 15367560
EST50 67067 29051138
EST51 73841 32839421
EST52 71404 30117948
EST53 80964 32886400
EST54 75516 29794973
EST55 71191 28656190
EST56 64472 29638724
EST57 75853 34147667
EST58 77187 34342037
EST59 74358 29349979
EST6 56332 18258994
EST60 77206 27172065
EST61 84976 39864820
EST62 40317 11538655
EST63 40273 11000858
EST64 40287 12450757
EST65 40629 12569723
EST66 40659 12253536
EST67 40569 12932595
EST68 40394 12889409
EST69 40599 12094067
EST7 74707 29422353
EST70 40255 12037430
EST71 41001 12778029
EST72 41529 11873769
EST73 41216 13143467
EST74 41056 12977804
EST75 42602 12984028
EST76 44809 15937926
EST77 40219 25297119
EST78 42282 20116896
EST79 47837 19338555
EST8 76830 30879168
EST80 51044 22831936
EST81 51541 21690057
EST82 67194 29877108
EST83 71901 27974431
EST84 75926 29803318
EST85 75234 40435377
EST86 78545 41879239
EST87 77972 44502583
EST88 75253 35130349
EST89 75935 43287188
EST9 77951 30110222
EST90 70928 36535683
EST91 75137 36603185
EST92 73696 41389694
EST93 74839 39302027
EST94 71048 40142489
EST95 68987 37029702
EST96 73912 37042854
EST97 72985 46140840
EST98 73559 45920473
EST99 70172 42891664
GSS1 91487 39178813
GSS10 75816 44130824
GSS100 75481 34977640
GSS101 91576 69234634
GSS102 95993 52973052
GSS103 78904 49215365
GSS104 74242 62612090
GSS105 69633 58620004
GSS106 67413 63586004
GSS107 66609 53496485
GSS108 104393 56042067
GSS109 108896 54167634
GSS11 69173 35579720
GSS110 43417 19063499
GSS12 74399 38991314
GSS13 74975 37674241
GSS14 72504 32438642
GSS15 73587 37366102
GSS16 75296 43832006
GSS17 70273 32348402
GSS18 57512 29348258
GSS19 57689 28843040
GSS2 89911 39770582
GSS20 58964 25524452
GSS21 63584 38702909
GSS22 63505 29995854
GSS23 58832 29908648
GSS24 72198 43165906
GSS25 63147 24485474
GSS26 58276 27277779
GSS27 74979 35066573
GSS28 56768 31099571
GSS29 91019 43133399
GSS3 88258 42112413
GSS30 78076 40681053
GSS31 74184 43644470
GSS32 71247 43894434
GSS33 81465 39863878
GSS34 76549 40894147
GSS35 81767 47395297
GSS36 94348 62695292
GSS37 90064 50970061
GSS38 94369 58108236
GSS39 83654 37342621
GSS4 79835 41569189
GSS40 86930 36322321
GSS41 82189 50060467
GSS42 81082 57579492
GSS43 74887 51421385
GSS44 72787 48096880
GSS45 73022 47731178
GSS46 80936 39526105
GSS47 83838 52874332
GSS48 92005 64539495
GSS49 80658 60377919
GSS5 79679 41076797
GSS50 93455 56902639
GSS51 89074 58217847
GSS52 79262 47957270
GSS53 72997 37711478
GSS54 88297 52485489
GSS55 88158 55383634
GSS56 79863 62780655
GSS57 72100 79164727
GSS58 84269 70878035
GSS59 91782 63710288
GSS6 78381 39036861
GSS60 64998 44082240
GSS61 64839 44888727
GSS62 89675 66737951
GSS63 87073 60904360
GSS64 87290 53326465
GSS65 88563 57675512
GSS66 96594 59482669
GSS67 101135 54424422
GSS68 100872 54757390
GSS69 101691 53723622
GSS7 77255 39700569
GSS70 102837 52275058
GSS71 102727 52413695
GSS72 102847 52263364
GSS73 102515 52681599
GSS74 99997 55840610
GSS75 90311 69246622
GSS76 89846 70763473
GSS77 88508 69923114
GSS78 88105 69874659
GSS79 89718 63069864
GSS8 77182 38154928
GSS80 83655 30747504
GSS81 78990 24738155
GSS82 87003 35369247
GSS83 83057 48797272
GSS84 81022 48137561
GSS85 89652 64356874
GSS86 79357 61815867
GSS87 77803 79550725
GSS88 78673 58277238
GSS89 91629 54713744
GSS9 72967 37474282
GSS90 87458 55891440
GSS91 72714 59422514
GSS92 59612 35058755
GSS93 88249 65635082
GSS94 84796 63613729
GSS95 102086 47442993
GSS96 75789 65171775
GSS97 76340 64169954
GSS98 77019 63007982
GSS99 77394 62362776
HTC1 32052 55423415
HTC2 31834 67306459
HTC3 86951 78840760
HTC4 20947 25680867
HTG1 1329 190552749
HTG10 1256 189094891
HTG11 1430 187551911
HTG12 905 192373957
HTG13 751 192651927
HTG14 745 192475833
HTG15 777 192736329
HTG16 800 192353437
HTG17 774 192490109
HTG18 1845 181733898
HTG19 1177 188793779
HTG2 2574 188255115
HTG20 998 190361894
HTG21 1094 189939505
HTG22 789 192223304
HTG23 915 191352848
HTG24 873 192186842
HTG25 897 191537891
HTG26 816 191955898
HTG27 785 192387570
HTG28 881 191840502
HTG29 893 192012857
HTG3 2486 188086194
HTG30 946 191278334
HTG31 958 191350958
HTG32 930 191492347
HTG33 972 191164578
HTG34 894 191939886
HTG35 886 192236245
HTG36 991 191148989
HTG37 884 191867325
HTG38 900 191820737
HTG39 828 192138389
HTG4 2521 189936699
HTG40 878 191714671
HTG41 930 191320232
HTG42 949 191781165
HTG43 937 191787504
HTG44 965 191564222
HTG45 1107 190391395
HTG46 1150 189608587
HTG47 1310 190291018
HTG48 1133 190848080
HTG49 1155 190063518
HTG5 1294 188245488
HTG50 1097 191046807
HTG51 1174 191546565
HTG52 1258 191965093
HTG53 1171 192192773
HTG54 1310 192037919
HTG55 1194 191939456
HTG56 1115 190873531
HTG57 1089 193890767
HTG58 1001 194483698
HTG59 1017 193725528
HTG6 1288 187970479
HTG60 1133 193123619
HTG61 1037 190665635
HTG62 84 8394015
HTG7 1262 188129966
HTG8 1302 187695362
HTG9 1190 189560588
INV1 12929 168740010
INV2 1356 167950230
INV3 56718 93132900
INV4 71996 76711088
INV5 43276 104304965
INV6 39470 87670432
MAM 60421 83578837
PAT1 223219 70408791
PAT10 108267 50638745
PAT11 151419 56282856
PAT12 157986 74549768
PAT13 103445 120727004
PAT14 146500 92069178
PAT15 114560 39690674
PAT2 199580 89443327
PAT3 163733 97025538
PAT4 154179 83573852
PAT5 107664 119373376
PAT6 144802 91232516
PAT7 126271 101537671
PAT8 145843 61509928
PAT9 104631 61049385
PHG 2510 12668047
PLN1 27790 130201006
PLN10 49452 111509292
PLN11 37345 114267581
PLN12 1205 2098490
PLN2 2258 178786688
PLN3 64291 93128966
PLN4 69460 70893454
PLN5 30404 57037745
PLN6 1454 172163410
PLN7 18707 137228501
PLN8 59218 72003614
PLN9 73383 76287330
PRI1 17411 152119736
PRI10 1405 176157572
PRI11 1273 175499086
PRI12 1497 175229415
PRI13 1590 178762533
PRI14 1519 184720749
PRI15 28872 144087231
PRI16 40577 88842912
PRI17 9343 160141549
PRI18 1602 180138153
PRI19 1747 181558550
PRI2 1421 173111031
PRI20 2205 187930178
PRI21 1472 186781377
PRI22 38920 113735447
PRI23 27230 95485838
PRI24 11673 172084588
PRI25 28193 141288827
PRI26 41719 123791110
PRI27 56014 104107811
PRI28 3182 5419678
PRI3 1257 182333250
PRI4 1293 178198566
PRI5 1144 173764460
PRI6 1202 178856128
PRI7 1213 177372978
PRI8 1328 169554514
PRI9 1229 177599460
ROD1 7573 173093806
ROD10 1355 193990031
ROD11 37301 82333051
ROD12 37846 130446921
ROD13 9217 12247707
ROD2 881 174475037
ROD3 897 176357225
ROD4 992 180407338
ROD5 983 180838371
ROD6 991 181622078
ROD7 25446 147520636
ROD8 1722 192633114
ROD9 1199 193116575
STS1 88885 48157763
STS2 74680 30673512
STS3 97643 38071473
STS4 85863 37146108
STS5 26579 11045933
SYN 11690 19955728
UNA 1271 557857
VRL1 72973 65390366
VRL2 73508 65243232
VRL3 75109 66105412
VRL4 13248 18820687
VRT1 65772 93256716
VRT2 10162 167981190
VRT3 63605 58846713
VRT4 41821 141046957
VRT5 1267 193868478
VRT6 45099 80439896
2.2.7 Selected Per-Organism Statistics
The following table provides the number of entries and bases of DNA/RNA for
the twenty most sequenced organisms in Release 142.0 (chloroplast and mitochon-
drial sequences not included, and Whole Genome Shotgun sequences not included) :
Entries Bases Species
7921258 10662673477 Homo sapiens
5679133 6510495187 Mus musculus
896664 5593182301 Rattus norvegicus
699938 1719817083 Danio rerio
2237983 1406301024 Zea mays
335133 750358559 Oryza sativa (japonica cultivar-group)
376823 708892835 Drosophila melanogaster
651079 546021688 Gallus gallus
722554 531217961 Arabidopsis thaliana
898189 518858629 Canis familiaris
761955 462899090 Bos taurus
193280 426456257 Pan troglodytes
691089 415026837 Ciona intestinalis
508360 413563897 Xenopus tropicalis
595911 403889442 Brassica oleracea
39521 360878971 Macaca mulatta
347927 315519485 Medicago truncatula
555611 304874306 Triticum aestivum
449798 286092539 Xenopus laevis
306304 281281799 Caenorhabditis elegans
2.2.8 Growth of GenBank
The following table lists the number of bases and the number of sequence
records in each release of GenBank, beginning with Release 3 in 1982.
From 1982 to the present, the number of bases in GenBank has doubled
approximately every 14 months.
Release Date Base Pairs Entries
3 Dec 1982 680338 606
14 Nov 1983 2274029 2427
20 May 1984 3002088 3665
24 Sep 1984 3323270 4135
25 Oct 1984 3368765 4175
26 Nov 1984 3689752 4393
32 May 1985 4211931 4954
36 Sep 1985 5204420 5700
40 Feb 1986 5925429 6642
42 May 1986 6765476 7416
44 Aug 1986 8442357 8823
46 Nov 1986 9615371 9978
48 Feb 1987 10961380 10913
50 May 1987 13048473 12534
52 Aug 1987 14855145 14020
53 Sep 1987 15514776 14584
54 Dec 1987 16752872 15465
55 Mar 1988 19156002 17047
56 Jun 1988 20795279 18226
57 Sep 1988 22019698 19044
57.1 Oct 1988 23800000 20579
58 Dec 1988 24690876 21248
59 Mar 1989 26382491 22479
60 Jun 1989 31808784 26317
61 Sep 1989 34762585 28791
62 Dec 1989 37183950 31229
63 Mar 1990 40127752 33377
64 Jun 1990 42495893 35100
65 Sep 1990 49179285 39533
66 Dec 1990 51306092 41057
67 Mar 1991 55169276 43903
68 Jun 1991 65868799 51418
69 Sep 1991 71947426 55627
70 Dec 1991 77337678 58952
71 Mar 1992 83894652 65100
72 Jun 1992 92160761 71280
73 Sep 1992 101008486 78608
74 Dec 1992 120242234 97084
75 Feb 1993 126212259 106684
76 Apr 1993 129968355 111911
77 Jun 1993 138904393 120134
78 Aug 1993 147215633 131328
79 Oct 1993 157152442 143492
80 Dec 1993 163802597 150744
81 Feb 1994 173261500 162946
82 Apr 1994 180589455 169896
83 Jun 1994 191393939 182753
84 Aug 1994 201815802 196703
85 Oct 1994 217102462 215273
86 Dec 1994 230485928 237775
87 Feb 1995 248499214 269478
88 Apr 1995 286094556 352414
89 Jun 1995 318624568 425211
90 Aug 1995 353713490 492483
91 Oct 1995 384939485 555694
92 Dec 1995 425860958 620765
93 Feb 1996 463758833 685693
94 Apr 1996 499127741 744295
95 Jun 1996 551750920 835487
96 Aug 1996 602072354 920588
97 Oct 1996 651972984 1021211
98 Dec 1996 730552938 1114581
99 Feb 1997 786898138 1192505
100 Apr 1997 842864309 1274747
101 Jun 1997 966993087 1491069
102 Aug 1997 1053474516 1610848
103 Oct 1997 1160300687 1765847
104 Dec 1997 1258290513 1891953
105 Feb 1998 1372368913 2042325
106 Apr 1998 1502542306 2209232
107 Jun 1998 1622041465 2355928
108 Aug 1998 1797137713 2532359
109 Oct 1998 2008761784 2837897
110 Dec 1998 2162067871 3043729
111 Apr 1999 2569578208 3525418
112 Jun 1999 2974791993 4028171
113 Aug 1999 3400237391 4610118
114 Oct 1999 3841163011 4864570
115 Dec 1999 4653932745 5354511
116 Feb 2000 5805414935 5691170
117 Apr 2000 7376080723 6215002
118 Jun 2000 8604221980 7077491
119 Aug 2000 9545724824 8214339
120 Oct 2000 10335692655 9102634
121 Dec 2000 11101066288 10106023
122 Feb 2001 11720120326 10896781
123 Apr 2001 12418544023 11545572
124 Jun 2001 12973707065 12243766
125 Aug 2001 13543364296 12813516
126 Oct 2001 14396883064 13602262
127 Dec 2001 15849921438 14976310
128 Feb 2002 17089143893 15465325
129 Apr 2002 19072679701 16769983
130 Jun 2002 20648748345 17471130
131 Aug 2002 22616937182 18197119
132 Oct 2002 26525934656 19808101
133 Dec 2002 28507990166 22318883
134 Feb 2003 29358082791 23035823
135 Apr 2003 31099264455 24027936
136 Jun 2003 32528249295 25592865
137 Aug 2003 33865022251 27213748
138 Oct 2003 35599621471 29819397
139 Dec 2003 36553368485 30968418
140 Feb 2004 37893844733 32549400
141 Apr 2004 38989342565 33676218
142 Jun 2004 40325321348 35532003
The following table lists the number of bases and the number of sequence
records for WGS sequences processed at GenBank, beginning with Release 129.0
in April of 2002.
Release Date Base Pairs Entries
129 Apr 2002 692266338 172768
130 Jun 2002 3267608441 397502
131 Aug 2002 3848375582 427771
132 Oct 2002 3892435593 434224
133 Dec 2002 6702372564 597042
134 Feb 2003 6705740844 597345
135 Apr 2003 6897080355 596818
136 Jun 2003 6992663962 607155
137 Aug 2003 7144761762 593801
138 Oct 2003 8662242833 1683437
139 Dec 2003 14523454868 2547094
140 Feb 2004 22804145885 3188754
141 Apr 2004 24758556215 4112532
142 Jun 2004 25592758366 4353890
3. FILE FORMATS
The flat file examples included in this section, while not always from the
current release, are usually fairly recent. Any differences compared to the
actual records are the result of updates to the entries involved.
3.1 File Header Information
With the exception of the index files, gbcon.seq, and the lists of new,
changed, and deleted accession numbers, each of the 634 files of a GenBank
release begins with the same header, except for the first line, which
contains the file name, and the sixth line, which contains the title of
the file. The first line of the file contains the file name in character
positions 1 to 9 and the full database name (Genetic Sequence Data Bank,
aka 'GenBank') starting in column 22. The brief names of the files in this
release are listed in section 2.2.
The second line contains the date of the current release in the form
`day month year', beginning in position 27. The fourth line contains
the current GenBank release number. The release number appears in
positions 48 to 52 and consists of three numbers separated by a decimal
point. The number to the left of the decimal is the major release
number. The digit to the right of the decimal indicates the version of
the major release; it is zero for the first version. The sixth line
contains a title for the file. The eighth line lists the number of
entries (loci), number of bases (or base pairs), and number of reports
of sequences (equal to number of entries in this case). These numbers are
right-justified at fixed positions. The number of entries appears in
positions 1 to 8, the number of bases in positions 16 to 26, and the
number of reports in positions 40 to 47. The third, fifth, seventh, and
ninth lines are blank.
1 10 20 30 40 50 60 70 79
---------+---------+---------+---------+---------+---------+---------+---------
GBBCT1.SEQ Genetic Sequence Data Bank
15 June 2004
NCBI-GenBank Flat File Release 142.0
Bacterial Sequences (Part 1)
37811 loci, 97585608 bases, from 37811 reported sequences
---------+---------+---------+---------+---------+---------+---------+---------
1 10 20 30 40 50 60 70 79
Example 1. Sample File Header
3.2 Directory Files
3.2.1 Short Directory File
The short directory file contains brief descriptions of all of the
sequence entries contained in this release. These descriptions are in
fifteen groups, one group for each of the fifteen sequence entry
data files. The first record at the beginning of a group of entries
contains the name of the group in uppercase characters, beginning in
position 21. The organism groups are PRIMATE, RODENT, OTHER MAMMAL,
OTHER VERTEBRATE, INVERTEBRATE, PLANT, BACTERIAL, STRUCTURAL RNA, VIRAL,
PHAGE, SYNTHETIC, UNANNOTATED, EXPRESSED SEQUENCE TAG, PATENT, or
SEQUENCE TAGGED SITE. The second record is blank.
Each record in the short directory contains the sequence entry name
(LOCUS) in the first 12 positions, followed by a brief definition of
the sequence beginning in column 13. The definition is truncated (at
the end of a word) to leave room at the right margin for at least one
space, the sequence length, and the letters `bp'. The length of the
sequence is printed right-justified to column 77, followed by the
letters `bp' in columns 78 and 79. The next-to-last record for a group
has `ZZZZZZZZZZ' in its first ten positions (where the entry name
would normally appear). The last record is a blank line. An example of
the short directory file format, showing the descriptions of the last
entries in the Other Vertebrate sequence data file and the first
entries of the Invertebrate sequence data file, is reproduced below:
1 10 20 30 40 50 60 70 79
---------+---------+---------+---------+---------+---------+---------+---------
ZEFWNT1G3 B.rerio wnt-1 gene (exon 3) for wnt-1 protein. 266bp
ZEFWNT1G4 B.rerio wnt-1 gene (exon 4) for wnt-1 protein. 647bp
ZEFZF54 Zebrafish homeotic gene ZF-54. 246bp
ZEFZFEN Zebrafish engrailed-like homeobox sequence. 327bp
ZZZZZZZZZZ
INVERTEBRATE
AAHAV33A Acanthocheilonema viteae pepsin-inhibitor-like-protein 1048bp
ACAAC01 Acanthamoeba castelani gene encoding actin I. 1571bp
ACAACTPH Acanthamoeba castellanii actophorin mRNA, complete cds. 671bp
ACAMHCA A.castellanii non-muscle myosin heavy chain gene, partial 5894bp
---------+---------+---------+---------+---------+---------+---------+---------
1 10 20 30 40 50 60 70 79
Example 2. Short Directory File
3.3 Index Files
There are six files containing indices to the entries in this release:
Accession number index file (Accession and Version)
Secondary accession number index file
Keyword phrase index file
Author name index file
Journal citation index file
Gene name index file
The index keys (accession numbers, keywords, authors, journals, and
gene symbols.) of an index are sorted alphabetically. All index keys
appear in uppercase characters even though they appear in mixed case
in the sequence entries. Following each index key, the identifiers of the
sequence entries containing that key are listed (LOCUS name,
division abbreviation, and primary accession number). The division
abbreviations are:
1. PRI - primate sequences
2. ROD - rodent sequences
3. MAM - other mammalian sequences
4. VRT - other vertebrate sequences
5. INV - invertebrate sequences
6. PLN - plant, fungal, and algal sequences
7. BCT - bacterial sequences
8. VRL - viral sequences
9. PHG - bacteriophage sequences
10. SYN - synthetic sequences
11. UNA - unannotated sequences
12. EST - EST sequences (expressed sequence tags)
13. PAT - patent sequences
14. STS - STS sequences (sequence tagged sites)
15. GSS - GSS sequences (genome survey sequences)
16. HTG - HTGS sequences (high throughput genomic sequences)
17. HTC - HTC sequences (high throughput cDNA sequences)
A line-oriented, TAB-delimited format is utilized for the gbaut.idx,
gbgen.idx, gbjou.idx, gbkey.idx, and gbsec.idx indexes. Each index
key is presented on its own line, and is followed by a
LOCUS/Division/Accession triplet for every record containing the key:
Indexed-Term
LOCUS-name1 Div-code1 Accession1
LOCUS-name2 Div-code2 Accession2
LOCUS-name3 Div-code3 Accession3
....
Here is an example of the format, in which TAB characters are displayed
as ^I, and carriage-returns/newlines as $ :
(H+,K+)-ATPASE BETA-SUBUNIT$
^IRATHKATPB^IROD^IM55655$
^IMUSATP4B1^IROD^IM64685$
^IMUSATP4B2^IROD^IM64686$
^IMUSATP4B3^IROD^IM64687$
^IMUSATP4B4^IROD^IM64688$
^IDOGATPASEB^IMAM^IM76486$
When viewed by a file browser such as 'less' or 'more' :
(H+,K+)-ATPASE BETA-SUBUNIT
RATHKATPB ROD M55655
MUSATP4B1 ROD M64685
MUSATP4B2 ROD M64686
MUSATP4B3 ROD M64687
MUSATP4B4 ROD M64688
DOGATPASEB MAM M76486
Note that the index keys can be distinguished from LOCUS/DIV/ACCESSION
by the fact that they do not start with a TAB character. So one can
extract just the terms via simple text-processing:
perl -ne 'print unless /^\s+/' < gbkey.idx > terms.gbkey
The format of the primary accession number index file is slightly
different, with each indexed key (Accession.Version) present on
the same line as the LOCUS/Division/Accession triplet:
Accession1.Version1 Locus-name1 Div-code1 Accession1
Accession2.Version2 Locus-name2 Div-code2 Accession2
....
Here is an example of the format, in which TAB characters are displayed
as ^I, and carriage-returns/newlines as $ :
AC000102.1^IAC000102^IPRI^IAC000102$
AC000103.1^IAC000103^IPLN^IAC000103$
AC000104.1^IF19P19^IPLN^IAC000104$
AC000105.40^IAC000105^IPRI^IAC000105$
AC000106.1^IF7G19^IPLN^IAC000106$
AC000107.1^IAC000107^IPLN^IAC000107$
AC000108.1^IAC000108^IBCT^IAC000108$
AC000109.1^IHSAC000109^IPRI^IAC000109$
AC000110.1^IHSAC000110^IPRI^IAC000110$
When viewed by a file browser such as 'less' or 'more' :
AC000102.1 AC000102 PRI AC000102
AC000103.1 AC000103 PLN AC000103
AC000104.1 F19P19 PLN AC000104
AC000105.40 AC000105 PRI AC000105
AC000106.1 F7G19 PLN AC000106
AC000107.1 AC000107 PLN AC000107
AC000108.1 AC000108 BCT AC000108
AC000109.1 HSAC000109 PRI AC000109
AC000110.1 HSAC000110 PRI AC000110
3.3.1 Accession Number Index File - gbacc.idx
Accession numbers are unique six character or eight-character alphanumeric
identifiers of GenBank database entries. The six-character accession
number format consists of a single uppercase letter, followed by 5 digits.
The eight-character accession number format consists of two uppercase
letters, followed by 6 digits. Accessions provide an unchanging identifier
for the data with which they are associated, and we encourage you to cite
accession numbers whenever you refer to data from GenBank.
GenBank entries can have both 'primary' and 'secondary' accessions
associated with them (see Section 3.5.6). Only primary accessions are present
in the gbacc.idx index.
3.3.2 Keyword Phrase Index File - gbkey.idx
Keyword phrases consist of names for gene products and other
characteristics of sequence entries.
3.3.3 Author Name Index File - gbaut*.idx
The author name index files list all of the author names that appear
in the references within sequence records.
3.3.4 Journal Citation Index File - gbjou.idx
The journal citation index file lists all of the citations that appear
in the references within sequence records.. All citations are truncated
to 80 characters.
3.3.5 Gene Name Index - gbgen.idx
The /gene qualifiers of many GenBank entries contain values other than
official gene symbols, such as the product or the standard name of the gene.
Hence, NCBI has chosen to build an index (gbgen.idx) more like a keyword index
for this field, using both the GenBank /gene qualifier and the 'Gene.locus'
fields from the NCBI internal database as keys.
3.4 Sequence Entry Files
GenBank releases contain one or more sequence entry data files, one
for each "division" of GenBank.
3.4.1 File Organization
Each of these files has the same format and consists of two parts:
header information (described in section 3.1) and sequence entries for
that division (described in the following sections).
3.4.2 Entry Organization
In the second portion of a sequence entry file (containing the
sequence entries for that division), each record (line) consists of
two parts. The first part is found in positions 1 to 10 and may
contain:
1. A keyword, beginning in column 1 of the record (e.g., REFERENCE is
a keyword).
2. A subkeyword beginning in column 3, with columns 1 and 2 blank
(e.g., AUTHORS is a subkeyword of REFERENCE). Or a subkeyword beginning
in column 4, with columns 1, 2, and 3 blank (e.g., PUBMED is a
subkeyword of REFERENCE).
3. Blank characters, indicating that this record is a continuation of
the information under the keyword or subkeyword above it.
4. A code, beginning in column 6, indicating the nature of an entry
(feature key) in the FEATURES table; these codes are described in
Section 3.4.12.1 below.
5. A number, ending in column 9 of the record. This number occurs in
the portion of the entry describing the actual nucleotide sequence and
designates the numbering of sequence positions.
6. Two slashes (//) in positions 1 and 2, marking the end of an entry.
The second part of each sequence entry record contains the information
appropriate to its keyword, in positions 13 to 80 for keywords and
positions 11 to 80 for the sequence.
The following is a brief description of each entry field. Detailed
information about each field may be found in Sections 3.4.4 to 3.4.14.
LOCUS - A short mnemonic name for the entry, chosen to suggest the
sequence's definition. Mandatory keyword/exactly one record.
DEFINITION - A concise description of the sequence. Mandatory
keyword/one or more records.
ACCESSION - The primary accession number is a unique, unchanging
code assigned to each entry. (Please use this code when citing
information from GenBank.) Mandatory keyword/one or more records.
VERSION - A compound identifier consisting of the primary
accession number and a numeric version number associated with the
current version of the sequence data in the record. This is followed
by an integer key (a "GI") assigned to the sequence by NCBI.
Mandatory keyword/exactly one record.
NID - An alternative method of presenting the NCBI GI
identifier (described above). The NID is obsolete and was removed
from the GenBank flatfile format in December 1999.
KEYWORDS - Short phrases describing gene products and other
information about an entry. Mandatory keyword in all annotated
entries/one or more records.
SEGMENT - Information on the order in which this entry appears in a
series of discontinuous sequences from the same molecule. Optional
keyword (only in segmented entries)/exactly one record.
SOURCE - Common name of the organism or the name most frequently used
in the literature. Mandatory keyword in all annotated entries/one or
more records/includes one subkeyword.
ORGANISM - Formal scientific name of the organism (first line)
and taxonomic classification levels (second and subsequent lines).
Mandatory subkeyword in all annotated entries/two or more records.
REFERENCE - Citations for all articles containing data reported
in this entry. Includes seven subkeywords and may repeat. Mandatory
keyword/one or more records.
AUTHORS - Lists the authors of the citation. Optional
subkeyword/one or more records.
CONSRTM - Lists the collective names of consortiums associated
with the citation (eg, International Human Genome Sequencing Consortium),
rather than individual author names. Optional subkeyword/one or more records.
TITLE - Full title of citation. Optional subkeyword (present
in all but unpublished citations)/one or more records.
JOURNAL - Lists the journal name, volume, year, and page
numbers of the citation. Mandatory subkeyword/one or more records.
MEDLINE - Provides the Medline unique identifier for a
citation. Optional subkeyword/one record.
PUBMED - Provides the PubMed unique identifier for a
citation. Optional subkeyword/one record.
REMARK - Specifies the relevance of a citation to an
entry. Optional subkeyword/one or more records.
COMMENT - Cross-references to other sequence entries, comparisons to
other collections, notes of changes in LOCUS names, and other remarks.
Optional keyword/one or more records/may include blank records.
FEATURES - Table containing information on portions of the
sequence that code for proteins and RNA molecules and information on
experimentally determined sites of biological significance. Optional
keyword/one or more records.
BASE COUNT - Summary of the number of occurrences of each base
code in the sequence. Mandatory keyword/exactly one record.
ORIGIN - Specification of how the first base of the reported sequence
is operationally located within the genome. Where possible, this
includes its location within a larger genetic map. Mandatory
keyword/exactly one record.
- The ORIGIN line is followed by sequence data (multiple records).
// - Entry termination symbol. Mandatory at the end of an
entry/exactly one record.
3.4.3 Sample Sequence Data File
An example of a complete sequence entry file follows. (This example
has only two entries.) Note that in this example, as throughout the
data bank, numbers in square brackets indicate items in the REFERENCE
list. For example, in ACARR58S, [1] refers to the paper by Mackay, et
al.
1 10 20 30 40 50 60 70 79
---------+---------+---------+---------+---------+---------+---------+---------
GBSMP.SEQ Genetic Sequence Data Bank
15 December 1992
GenBank Flat File Release 74.0
Structural RNA Sequences
2 loci, 236 bases, from 2 reported sequences
LOCUS AAURRA 118 bp ss-rRNA RNA 16-JUN-1986
DEFINITION A.auricula-judae (mushroom) 5S ribosomal RNA.
ACCESSION K03160
VERSION K03160.1 GI:173593
KEYWORDS 5S ribosomal RNA; ribosomal RNA.
SOURCE A.auricula-judae (mushroom) ribosomal RNA.
ORGANISM Auricularia auricula-judae
Eukaryota; Fungi; Eumycota; Basidiomycotina; Phragmobasidiomycetes;
Heterobasidiomycetidae; Auriculariales; Auriculariaceae.
REFERENCE 1 (bases 1 to 118)
AUTHORS Huysmans,E., Dams,E., Vandenberghe,A. and De Wachter,R.
TITLE The nucleotide sequences of the 5S rRNAs of four mushrooms and
their use in studying the phylogenetic position of basidiomycetes
among the eukaryotes
JOURNAL Nucleic Acids Res. 11, 2871-2880 (1983)
FEATURES Location/Qualifiers
rRNA 1..118
/note="5S ribosomal RNA"
BASE COUNT 27 a 34 c 34 g 23 t
ORIGIN 5' end of mature rRNA.
1 atccacggcc ataggactct gaaagcactg catcccgtcc gatctgcaaa gttaaccaga
61 gtaccgccca gttagtacca cggtggggga ccacgcggga atcctgggtg ctgtggtt
//
LOCUS ABCRRAA 118 bp ss-rRNA RNA 15-SEP-1990
DEFINITION Acetobacter sp. (strain MB 58) 5S ribosomal RNA, complete sequence.
ACCESSION M34766
VERSION M34766.1 GI:173603
KEYWORDS 5S ribosomal RNA.
SOURCE Acetobacter sp. (strain MB 58) rRNA.
ORGANISM Acetobacter sp.
Prokaryotae; Gracilicutes; Scotobacteria; Aerobic rods and cocci;
Azotobacteraceae.
REFERENCE 1 (bases 1 to 118)
AUTHORS Bulygina,E.S., Galchenko,V.F., Govorukhina,N.I., Netrusov,A.I.,
Nikitin,D.I., Trotsenko,Y.A. and Chumakov,K.M.
TITLE Taxonomic studies of methylotrophic bacteria by 5S ribosomal RNA
sequencing
JOURNAL J. Gen. Microbiol. 136, 441-446 (1990)
FEATURES Location/Qualifiers
rRNA 1..118
/note="5S ribosomal RNA"
BASE COUNT 27 a 40 c 32 g 17 t 2 others
ORIGIN
1 gatctggtgg ccatggcggg agcaaatcag ccgatcccat cccgaactcg gccgtcaaat
61 gccccagcgc ccatgatact ctgcctcaag gcacggaaaa gtcggtcgcc gccagayy
//
---------+---------+---------+---------+---------+---------+---------+---------
1 10 20 30 40 50 60 70 79
Example 9. Sample Sequence Data File
3.4.4 LOCUS Format
The items of information contained in the LOCUS record are always
found in fixed positions. The locus name (or entry name), which is
always sixteen characters or less, begins in position 13. The locus name
is designed to help group entries with similar sequences: the first
three characters usually designate the organism; the fourth and fifth
characters can be used to show other group designations, such as gene
product; for segmented entries the last character is one of a series
of sequential integers.
The number of bases or base pairs in the sequence ends in position 40.
The letters `bp' are in positions 42 to 43. Positions 45 to 47 provide
the number of strands of the sequence. Positions 48 to 53 indicate the
type of molecule sequenced. Topology of the molecule is indicated in
positions 56 to 63.
GenBank sequence entries are divided among many different
'divisions'. Each entry's division is specified by a three-letter code
in positions 65 to 67. See Section 3.3 for an explanation of division
codes.
Positions 69 to 79 of the record contain the date the entry was
entered or underwent any substantial revisions, such as the addition
of newly published data, in the form dd-MMM-yyyy.
The detailed format for the LOCUS line format is as follows:
Positions Contents
--------- --------
01-05 'LOCUS'
06-12 spaces
13-28 Locus name
29-29 space
30-40 Length of sequence, right-justified
41-41 space
42-43 bp
44-44 space
45-47 spaces, ss- (single-stranded), ds- (double-stranded), or
ms- (mixed-stranded)
48-53 NA, DNA, RNA, tRNA (transfer RNA), rRNA (ribosomal RNA),
mRNA (messenger RNA), uRNA (small nuclear RNA), snRNA,
snoRNA. Left justified.
54-55 space
56-63 'linear' followed by two spaces, or 'circular'
64-64 space
65-67 The division code (see Section 3.3)
68-68 space
69-79 Date, in the form dd-MMM-yyyy (e.g., 15-MAR-1991)
Although each of these data values can be found at column-specific
positions, we encourage those who parse the contents of the LOCUS
line to use a token-based approach. This will prevent the need for
software changes if the spacing of the data values ever has to be
modified.
3.4.5 DEFINITION Format
The DEFINITION record gives a brief description of the sequence,
proceeding from general to specific. It starts with the common name of
the source organism, then gives the criteria by which this sequence is
distinguished from the remainder of the source genome, such as the
gene name and what it codes for, or the protein name and mRNA, or some
description of the sequence's function (if the sequence is
non-coding). If the sequence has a coding region, the description may
be followed by a completeness qualifier, such as cds (complete coding
sequence). There is no limit on the number of lines that may be part
of the DEFINITION. The last line must end with a period.
3.4.5.1 DEFINITION Format for NLM Entries
The DEFINITION line for entries derived from journal-scanning at the NLM is
an automatically generated descriptive summary that accompanies each DNA and
protein sequence. It contains information derived from fields in a database
that summarize the most important attributes of the sequence. The DEFINITION
lines are designed to supplement the accession number and the sequence itself
as a means of uniquely and completely specifying DNA and protein sequences. The
following are examples of NLM DEFINITION lines:
NADP-specific isocitrate dehydrogenase [swine, mRNA, 1 gene, 1585 nt]
94 kda fiber cell beaded-filament structural protein [rats, lens, mRNA
Partial, 1 gene, 1873 nt]
inhibin alpha {promoter and exons} [mice, Genomic, 1 gene, 1102 nt, segment
1 of 2]
cefEF, cefG=acetyl coenzyme A:deacetylcephalosporin C o-acetyltransferase
[Acremonium chrysogenum, Genomic, 2 genes, 2639 nt]
myogenic factor 3, qmf3=helix-loop-helix protein [Japanese quails,
embryo, Peptide Partial, 246 aa]
The first part of the definition line contains information describing
the genes and proteins represented by the molecular sequences. This can
be gene locus names, protein names and descriptions that replace or augment
actual names. Gene and gene product are linked by "=". Any special
identifying terms are presented within brackets, such as: {promoter},
{N-terminal}, {EC 2.13.2.4}, {alternatively spliced}, or {3' region}.
The second part of the definition line is delimited by square brackets, '[]',
and provides details about the molecule type and length. The biological
source, i.e., genus and species or common name as cited by the author.
Developmental stage, tissue type and strain are included if available.
The molecule types include: Genomic, mRNA, Peptide. and Other Genomic
Material. Genomic molecules are assumed to be partial sequence unless
"Complete" is specified, whereas mRNA and peptide molecules are assumed
to be complete unless "Partial" is noted.
3.4.6 ACCESSION Format
This field contains a series of six-character and/or eight-character
identifiers called 'accession numbers'. The six-character accession
number format consists of a single uppercase letter, followed by 5 digits.
The eight-character accession number format consists of two uppercase
letters, followed by 6 digits. The 'primary', or first, of the accession
numbers occupies positions 13 to 18 (6-character format) or positions
13 to 20 (8-character format). Subsequent 'secondary' accession numbers
(if present) are separated from the primary, and from each other, by a
single space. In some cases, multiple lines of secondary accession
numbers might be present, starting at position 13.
The primary accession number of a GenBank entry provides a stable identifier
for the biological object that the entry represents. Accessions do not change
when the underlying sequence data or associated features change.
Secondary accession numbers arise for a number of reasons. For example, a
single accession number may initially be assigned to a sequence described in
a publication. If it is later discovered that the sequence must be entered
into the database as multiple entries, each entry would receive a new primary
accession number, and the original accession number would appear as a secondary
accession number on each of the new entries.
3.4.7 VERSION Format
This line contains two types of identifiers for a GenBank database entry:
a compound accession number and an NCBI GI identifier.
LOCUS AF181452 1294 bp DNA PLN 12-OCT-1999
DEFINITION Hordeum vulgare dehydrin (Dhn2) gene, complete cds.
ACCESSION AF181452
VERSION AF181452.1 GI:6017929
^^^^^^^^^^ ^^^^^^^^^^
Compound NCBI GI
Accession Identifier
Number
A compound accession number consists of two parts: a stable, unchanging
primary-accession number portion (see Section 3.4.6 for a description of
accession numbers), and a sequentially increasing numeric version number.
The accession and version numbers are separated by a period. The initial
version number assigned to a new sequence is one. Compound accessions are
often referred to as "Accession.Version" .
An accession number allows one to retrieve the same biological object in the
database, regardless of any changes that are made to the entry over time. But
those changes can include changes to the sequence data itself, which is of
fundamental importance to many database users. So a numeric version number is
associated with the sequence data in every database entry. If an entry (for
example, AF181452) undergoes two sequence changes, its compound accession
number on the VERSION line would start as AF181452.1 . After the first sequence
change this would become: AF181452.2 . And after the second change: AF181452.3 .
The NCBI GI identifier of the VERSION line also serves as a method for
identifying the sequence data that has existed for a database entry over
time. GI identifiers are numeric values of one or more digits. Since they
are integer keys, they are less human-friendly than the Accession.Version
system described above. Returning to our example for AF181452, it was
initially assigned GI 6017929. If the sequence changes, a new integer GI will
be assigned, perhaps 7345003 . And after the second sequence change, perhaps
the GI would become 10456892 .
Why are both these methods for identifying the version of the sequence
associated with a database entry in use? For two reasons:
- Some data sources processed by NCBI for incorporation into its Entrez
sequence retrieval system do not version their own sequences.
- GIs provide a uniform, integer identifier system for every sequence
NCBI has processed. Some products and systems derived from (or reliant
upon) NCBI products and services prefer to use these integer identifiers
because they can all be processed in the same manner.
GenBank Releases contain only the most recent versions of all sequences
in the database. However, older versions can be obtained via GI-based or
Accession.Version-based queries with NCBI's web-Entrez and network-Entrez
applications. A sequence revision history web page is also available:
http://www.ncbi.nlm.nih.gov/htbin-post/Entrez/girevhist
NOTE: All the version numbers for the compound Accession.Version identifier
system were initialized to a value of one in February 1999, when that
system was introduced.
3.4.8 KEYWORDS Format
The KEYWORDS field does not appear in unannotated entries, but is
required in all annotated entries. Keywords are separated by
semicolons; a "keyword" may be a single word or a phrase consisting of
several words. Each line in the keywords field ends in a semicolon;
the last line ends with a period. If no keywords are included in the
entry, the KEYWORDS record contains only a period.
3.4.9 SEGMENT Format
The SEGMENT keyword is used when two (or more) entries of known
relative orientation are separated by a short (<10 kb) stretch of DNA.
It is limited to one line of the form `n of m', where `n' is the
segment number of the current entry and `m' is the total number of
segments.
3.4.10 SOURCE Format
The SOURCE field consists of two parts. The first part is found after
the SOURCE keyword and contains free-format information including an
abbreviated form of the organism name followed by a molecule type;
multiple lines are allowed, but the last line must end with a period.
The second part consists of information found after the ORGANISM
subkeyword. The formal scientific name for the source organism (genus
and species, where appropriate) is found on the same line as ORGANISM.
The records following the ORGANISM line list the taxonomic
classification levels, separated by semicolons and ending with a
period.
3.4.11 REFERENCE Format
The REFERENCE field consists of five parts: the keyword REFERENCE, and
the subkeywords AUTHORS, TITLE (optional), JOURNAL, MEDLINE (optional),
PUBMED (optional), and REMARK (optional).
The REFERENCE line contains the number of the particular reference and
(in parentheses) the range of bases in the sequence entry reported in
this citation. Additional prose notes may also be found within the
parentheses. The numbering of the references does not reflect
publication dates or priorities.
The AUTHORS line lists the authors in the order in which they appear
in the cited article. Last names are separated from initials by a
comma (no space); there is no comma before the final `and'. The list
of authors ends with a period. The TITLE line is an optional field,
although it appears in the majority of entries. It does not appear in
unpublished sequence data entries that have been deposited directly
into the GenBank data bank, the EMBL Nucleotide Sequence Data Library,
or the DNA Data Bank of Japan. The TITLE field does not end with a
period.
The JOURNAL line gives the appropriate literature citation for the
sequence in the entry. The word `Unpublished' will appear after the
JOURNAL subkeyword if the data did not appear in the scientific
literature, but was directly deposited into the data bank. For
published sequences the JOURNAL line gives the Thesis, Journal, or
Book citation, including the year of publication, the specific
citation, or In press.
For Book citations, the JOURNAL line is specially-formatted, and
includes:
editor name(s)
book title
page number(s)
publisher-name/publisher-location
year
For example:
LOCUS AY277550 1440 bp DNA linear BCT 17-JUN-2003
DEFINITION Stenotrophomonas maltophilia strain CSC13-6 16S ribosomal RNA gene,
partial sequence.
ACCESSION AY277550
....
REFERENCE 1 (bases 1 to 1440)
AUTHORS Gonzalez,J.M., Laiz,L. and Saiz-Jimenez,C.
TITLE Classifying bacterial isolates from hypogean environments:
Application of a novel fluorimetric method dor the estimation of
G+C mol% content in microorganisms by thermal denaturation
temperature
JOURNAL (in) Saiz-Jimenez,C. (Ed.);
MOLECULAR BIOLOGY AND CULTURAL HERITAGE: 47-54;
A.A. Balkema, The Netherlands (2003)
The presence of "(in)" signals the fact that the reference is for a book
rather than a journal article. A semi-colon signals the end of the editor
names. The next semi-colon signals the end of the page numbers, and the
colon that immediately *precedes* the page numbers signals the end of the
book title. The publisher name and location are a free-form text string.
Finally, the year appears at the very end of the JOURNAL line, enclosed in
parentheses.
The MEDLINE line provides the National Library of Medicine's Medline
unique identifier for a citation (if known). Medline UIs are 8 digit
numbers.
The PUBMED line provides the PubMed unique identifier for a citation
(if known). PUBMED ids are numeric, and are record identifiers for article
abstracts in the PubMed database :
http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed
Citations in PubMed that do not fall within Medline's scope will have only
a PUBMED identifier. Similarly, citations that *are* in Medline's scope but
which have not yet been assigned Medline UIs will have only a PUBMED identifier.
If a citation is present in both the PubMed and Medline databases, both a
MEDLINE and a PUBMED line will be present.
The REMARK line is a textual comment that specifies the relevance
of the citation to the entry.
3.4.12 FEATURES Format
GenBank releases use a feature table format designed jointly by
GenBank, the EMBL Nucleotide Sequence Data Library, and the DNA Data
Bank of Japan. This format is in use by all three databases. The
most complete and accurate Feature Table documentation can be found
on the Web at:
http://www.ncbi.nlm.nih.gov/projects/collab/FT/index.html
Any discrepancy between the abbreviated feature table description
of these release notes and the complete documentation on the Web
should be resolved in favor of the version at the above URL.
The Feature Table specification is also available as a printed
document: `The DDBJ/EMBL/GenBank Feature Table: Definition'. Contact
GenBank at the address shown on the first page of these Release Notes
if you would like a copy.
The feature table contains information about genes and gene products,
as well as regions of biological significance reported in the
sequence. The feature table contains information on regions of the
sequence that code for proteins and RNA molecules. It also enumerates
differences between different reports of the same sequence, and
provides cross-references to other data collections, as described in
more detail below.
The first line of the feature table is a header that includes the
keyword `FEATURES' and the column header `Location/Qualifier.' Each
feature consists of a descriptor line containing a feature key and a
location (see sections below for details). If the location does not
fit on this line, a continuation line may follow. If further
information about the feature is required, one or more lines
containing feature qualifiers may follow the descriptor line.
The feature key begins in column 6 and may be no more than 15
characters in length. The location begins in column 22. Feature
qualifiers begin on subsequent lines at column 22. Location,
qualifier, and continuation lines may extend from column 22 to 80.
Feature tables are required, due to the mandatory presence of the
source feature. The sections below provide a brief introduction to
the feature table format.
3.4.12.1 Feature Key Names
The first column of the feature descriptor line contains the feature
key. It starts at column 6 and can continue to column 20. The list of
valid feature keys is shown below.
Remember, the most definitive documentation for the feature table can
be found at:
http://www.ncbi.nlm.nih.gov/projects/collab/FT/index.html
allele Obsolete; see variation feature key
attenuator Sequence related to transcription termination
C_region Span of the C immunological feature
CAAT_signal `CAAT box' in eukaryotic promoters
CDS Sequence coding for amino acids in protein (includes
stop codon)
conflict Independent sequence determinations differ
D-loop Displacement loop
D_segment Span of the D immunological feature
enhancer Cis-acting enhancer of promoter function
exon Region that codes for part of spliced mRNA
gene Region that defines a functional gene, possibly
including upstream (promotor, enhancer, etc)
and downstream control elements, and for which
a name has been assigned.
GC_signal `GC box' in eukaryotic promoters
iDNA Intervening DNA eliminated by recombination
intron Transcribed region excised by mRNA splicing
J_region Span of the J immunological feature
LTR Long terminal repeat
mat_peptide Mature peptide coding region (does not include stop codon)
misc_binding Miscellaneous binding site
misc_difference Miscellaneous difference feature
misc_feature Region of biological significance that cannot be described
by any other feature
misc_recomb Miscellaneous recombination feature
misc_RNA Miscellaneous transcript feature not defined by other RNA keys
misc_signal Miscellaneous signal
misc_structure Miscellaneous DNA or RNA structure
modified_base The indicated base is a modified nucleotide
mRNA Messenger RNA
mutation Obsolete: see variation feature key
N_region Span of the N immunological feature
old_sequence Presented sequence revises a previous version
polyA_signal Signal for cleavage & polyadenylation
polyA_site Site at which polyadenine is added to mRNA
precursor_RNA Any RNA species that is not yet the mature RNA product
prim_transcript Primary (unprocessed) transcript
primer Primer binding region used with PCR
primer_bind Non-covalent primer binding site
promoter A region involved in transcription initiation
protein_bind Non-covalent protein binding site on DNA or RNA
RBS Ribosome binding site
rep_origin Replication origin for duplex DNA
repeat_region Sequence containing repeated subsequences
repeat_unit One repeated unit of a repeat_region
rRNA Ribosomal RNA
S_region Span of the S immunological feature
satellite Satellite repeated sequence
scRNA Small cytoplasmic RNA
sig_peptide Signal peptide coding region
snRNA Small nuclear RNA
source Biological source of the sequence data represented by
a GenBank record. Mandatory feature, one or more per record.
For organisms that have been incorporated within the
NCBI taxonomy database, an associated /db_xref="taxon:NNNN"
qualifier will be present (where NNNNN is the numeric
identifier assigned to the organism within the NCBI taxonomy
database).
stem_loop Hair-pin loop structure in DNA or RNA
STS Sequence Tagged Site; operationally unique sequence that
identifies the combination of primer spans used in a PCR assay
TATA_signal `TATA box' in eukaryotic promoters
terminator Sequence causing transcription termination
transit_peptide Transit peptide coding region
transposon Transposable element (TN)
tRNA Transfer RNA
unsure Authors are unsure about the sequence in this region
V_region Span of the V immunological feature
variation A related population contains stable mutation
- (hyphen) Placeholder
-10_signal `Pribnow box' in prokaryotic promoters
-35_signal `-35 box' in prokaryotic promoters
3'clip 3'-most region of a precursor transcript removed in processing
3'UTR 3' untranslated region (trailer)
5'clip 5'-most region of a precursor transcript removed in processing
5'UTR 5' untranslated region (leader)
3.4.12.2 Feature Location
The second column of the feature descriptor line designates the
location of the feature in the sequence. The location descriptor
begins at position 22. Several conventions are used to indicate
sequence location.
Base numbers in location descriptors refer to numbering in the entry,
which is not necessarily the same as the numbering scheme used in the
published report. The first base in the presented sequence is numbered
base 1. Sequences are presented in the 5 to 3 direction.
Location descriptors can be one of the following:
1. A single base;
2. A contiguous span of bases;
3. A site between two bases;
4. A single base chosen from a range of bases;
5. A single base chosen from among two or more specified bases;
6. A joining of sequence spans;
7. A reference to an entry other than the one to which the feature
belongs (i.e., a remote entry), followed by a location descriptor
referring to the remote sequence;
A site between two residues, such as an endonuclease cleavage site, is
indicated by listing the two bases separated by a carat (e.g., 23^24).
A single residue chosen from a range of residues is indicated by the
number of the first and last bases in the range separated by a single
period (e.g., 23.79). The symbols < and > indicate that the end point
of the range is beyond the specified base number.
A contiguous span of bases is indicated by the number of the first and
last bases in the range separated by two periods (e.g., 23..79). The
symbols < and > indicate that the end point of the range is beyond the
specified base number. Starting and ending positions can be indicated
by base number or by one of the operators described below.
Operators are prefixes that specify what must be done to the indicated
sequence to locate the feature. The following are the operators
available, along with their most common format and a description.
complement (location): The feature is complementary to the location
indicated. Complementary strands are read 5 to 3.
join (location, location, .. location): The indicated elements should
be placed end to end to form one contiguous sequence.
order (location, location, .. location): The elements are found in the
specified order in the 5 to 3 direction, but nothing is implied about
the rationality of joining them.
3.4.12.3 Feature Qualifiers
Qualifiers provide additional information about features. They take
the form of a slash (/) followed by a qualifier name and, if
applicable, an equal sign (=) and a qualifier value. Feature
qualifiers begin at column 22.
Qualifiers convey many types of information. Their values can,
therefore, take several forms:
1. Free text;
2. Controlled vocabulary or enumerated values;
3. Citations or reference numbers;
4. Sequences;
5. Feature labels.
Text qualifier values must be enclosed in double quotation marks. The
text can consist of any printable characters (ASCII values 32-126
decimal). If the text string includes double quotation marks, each set
must be `escaped' by placing a double quotation mark in front of it
(e.g., /note="This is an example of ""escaped"" quotation marks").
Some qualifiers require values selected from a limited set of choices.
For example, the `/direction' qualifier has only three values `left,'
`right,' or `both.' These are called controlled vocabulary qualifier
values. Controlled qualifier values are not case sensitive; they can
be entered in any combination of upper- and lowercase without changing
their meaning.
Citation or published reference numbers for the entry should be
enclosed in square brackets ([]) to distinguish them from other
numbers.
A literal sequence of bases (e.g., "atgcatt") should be enclosed in
quotation marks. Literal sequences are distinguished from free text by
context. Qualifiers that take free text as their values do not take
literal sequences, and vice versa.
The `/label=' qualifier takes a feature label as its qualifier.
Although feature labels are optional, they allow unambiguous
references to the feature. The feature label identifies a feature
within an entry; when combined with the accession number and the name
of the data bank from which it came, it is a unique tag for that
feature. Feature labels must be unique within an entry, but can be the
same as a feature label in another entry. Feature labels are not case
sensitive; they can be entered in any combination of upper-and
lowercase without changing their meaning.
The following is a partial list of feature qualifiers.
/anticodon Location of the anticodon of tRNA and the amino acid
for which it codes
/bound_moiety Moiety bound
/citation Reference to a citation providing the claim of or
evidence for a feature
/codon Specifies a codon that is different from any found in the
reference genetic code
/codon_start Indicates the first base of the first complete codon
in a CDS (as 1 or 2 or 3)
/cons_splice Identifies intron splice sites that do not conform to
the 5'-GT... AG-3' splice site consensus
/db_xref A database cross-reference; pointer to related information
in another database. A description of all cross-references
can be found at:
http://www.ncbi.nlm.nih.gov/collab/db_xref.html
/direction Direction of DNA replication
/EC_number Enzyme Commission number for the enzyme product of the
sequence
/evidence Value indicating the nature of supporting evidence
/frequency Frequency of the occurrence of a feature
/function Function attributed to a sequence
/gene Symbol of the gene corresponding to a sequence region (usable
with all features)
/label A label used to permanently identify a feature
/map Map position of the feature in free-format text
/mod_base Abbreviation for a modified nucleotide base
/note Any comment or additional information
/number A number indicating the order of genetic elements
(e.g., exons or introns) in the 5 to 3 direction
/organism Name of the organism that is the source of the
sequence data in the record.
/partial Differentiates between complete regions and partial ones
/phenotype Phenotype conferred by the feature
/product Name of a product encoded by a coding region (CDS)
feature
/pseudo Indicates that this feature is a non-functional
version of the element named by the feature key
/rpt_family Type of repeated sequence; Alu or Kpn, for example
/rpt_type Organization of repeated sequence
/rpt_unit Identity of repeat unit that constitutes a repeat_region
/standard_name Accepted standard name for this feature
/transl_except Translational exception: single codon, the translation
of which does not conform to the reference genetic code
/translation Amino acid translation of a coding region
/type Name of a strain if different from that in the SOURCE field
/usedin Indicates that feature is used in a compound feature
in another entry
3.4.12.4 Cross-Reference Information
One type of information in the feature table lists cross-references to
the annual compilation of transfer RNA sequences in Nucleic Acids
Research, which has kindly been sent to us on CD-ROM by Dr. Sprinzl.
Each tRNA entry of the feature table contains a /note= qualifier that
includes a reference such as `(NAR: 1234)' to identify code 1234 in
the NAR compilation. When such a cross-reference appears in an entry
that contains a gene coding for a transfer RNA molecule, it refers to
the code in the tRNA gene compilation. Similar cross-references in
entries containing mature transfer RNA sequences refer to the
companion compilation of tRNA sequences published by D.H. Gauss and M.
Sprinzl in Nucleic Acids Research.
3.4.12.5 Feature Table Examples
In the first example a number of key names, feature locations, and
qualifiers are illustrated, taken from different sequences. The first
table entry is a coding region consisting of a simple span of bases
and including a /gene qualifier. In the second table entry, an NAR
cross-reference is given (see the previous section for a discussion of
these cross-references). The third and fourth table entries use the
symbols `<`and `>' to indicate that the beginning or end of the
feature is beyond the range of the presented sequence. In the fifth
table entry, the symbol `^' indicates that the feature is between
bases.
1 10 20 30 40 50 60 70 79
---------+---------+---------+---------+---------+---------+---------+---------
CDS 5..1261
/product="alpha-1-antitrypsin precursor"
/map="14q32.1"
/gene="PI"
tRNA 1..87
/note="Leu-tRNA-CAA (NAR: 1057)"
/anticodon=(pos:35..37,aa:Leu)
mRNA 1..>66
/note="alpha-1-acid glycoprotein mRNA"
transposon <1..267
/note="insertion element IS5"
misc_recomb 105^106
/note="B.subtilis DNA end/IS5 DNA start"
conflict 258
/replace="t"
/citation=[2]
---------+---------+---------+---------+---------+---------+---------+---------
1 10 20 30 40 50 60 70 79
Example 10. Feature Table Entries
The next example shows the representation for a CDS that spans more
than one entry.
1 10 20 30 40 50 60 70 79
---------+---------+---------+---------+---------+---------+---------+---------
LOCUS HUMPGAMM1 3688 bp ds-DNA PRI 15-OCT-1990
DEFINITION Human phosphoglycerate mutase (muscle specific isozyme) (PGAM-M)
gene, 5' end.
ACCESSION M55673 M25818 M27095
KEYWORDS phosphoglycerate mutase.
SEGMENT 1 of 2
.
.
.
FEATURES Location/Qualifiers
CAAT_signal 1751..1755
/gene="PGAM-M"
TATA_signal 1791..1799
/gene="PGAM-M"
exon 1820..2274
/number=1
/EC_number="5.4.2.1"
/gene="PGAM-M"
intron 2275..2377
/number=1
/gene="PGAM2"
exon 2378..2558
/number=2
/gene="PGAM-M"
.
.
.
//
LOCUS HUMPGAMM2 677 bp ds-DNA PRI 15-OCT-1990
DEFINITION Human phosphoglycerate mutase (muscle specific isozyme) (PGAM-M),
exon 3.
ACCESSION M55674 M25818 M27096
KEYWORDS phosphoglycerate mutase.
SEGMENT 2 of 2
.
.
.
FEATURES Location/Qualifiers
exon 255..457
/number=3
/gene="PGAM-M"
intron order(M55673:2559..>3688,<1..254)
/number=2
/gene="PGAM-M"
mRNA join(M55673:1820..2274,M55673:2378..2558,255..457)
/gene="PGAM-M"
CDS join(M55673:1861..2274,M55673:2378..2558,255..421)
/note="muscle-specific isozyme"
/gene="PGAM2"
/product="phosphoglycerate mutase"
/codon_start=1
/translation="MATHRLVMVRHGESTWNQENRFCGWFDAELSEKGTEEAKRGAKA
IKDAKMEFDICYTSVLKRAIRTLWAILDGTDQMWLPVVRTWRLNERHYGGLTGLNKAE
TAAKHGEEQVKIWRRSFDIPPPPMDEKHPYYNSISKERRYAGLKPGELPTCESLKDTI
ARALPFWNEEIVPQIKAGKRVLIAAHGNSLRGIVKHLEGMSDQAIMELNLPTGIPIVY
ELNKELKPTKPMQFLGDEETVRKAMEAVAAQGKAK"
.
.
.
//
---------+---------+---------+---------+---------+---------+---------+---------
1 10 20 30 40 50 60 70 79
Example 11. Joining Sequences
3.4.13 ORIGIN Format
The ORIGIN record may be left blank, may appear as `Unreported.' or
may give a local pointer to the sequence start, usually involving an
experimentally determined restriction cleavage site or the genetic
locus (if available). The ORIGIN record ends in a period if it
contains data, but does not include the period if the record is left
empty (in contrast to the KEYWORDS field which contains a period
rather than being left blank).
3.4.14 SEQUENCE Format
The nucleotide sequence for an entry is found in the records following
the ORIGIN record. The sequence is reported in the 5 to 3 direction.
There are sixty bases per record, listed in groups of ten bases
followed by a blank, starting at position 11 of each record. The
number of the first nucleotide in the record is given in columns 4 to
9 (right justified) of the record.
4. ALTERNATE RELEASES
NCBI is supplying sequence data in the GenBank flat file format to
maintain compatibility with existing software which require that
particular format. Although we have made every effort to ensure
that these data are presented in the traditional flat file format,
if you encounter any problems in using these data with software which
is based upon the flat file format, please contact us at:
[email protected]
The flat file is just one of many possible report formats that can be
generated from the richer representation supported by the ASN.1 form of the
data. Developers of new software tools should consider using the ASN.1 form
directly to take advantage of those features. Documentation and a Software
Developer's Toolkit for ASN.1 are available through NCBI. You may call NCBI
at (301)496-2475, or subscribe to a developers' electronic newsgroup by
sending your name, address, affiliation, and e-mail address to:
[email protected]
The Software Developer's Toolkit and PostScript documentation for UNIX,
VMS, Ultrix, AIX, MacOS, DOS, and Microsoft Windows systems is available
in a compressed UNIX tar file by anonymous ftp from 'ftp.ncbi.nih.gov',
in the toolbox/ncbi_tools directory. The file is 'ncbi.tar.Z'.
5. KNOWN PROBLEMS OF THE GENBANK DATABASE
5.1 Incorrect Gene Symbols in Entries and Index
The /gene qualifier for many GenBank entries contains values other than the
official gene symbol, such as the product or the standard name of the gene. The
gene symbol index (gbgen.idx) is created from the data in the /gene qualifier
and therefore may contain data other than official gene symbols.
6. GENBANK ADMINISTRATION
The National Center for Biotechnology Information (NCBI), National Library
of Medicine, National Institutes of Health, is responsible for the production
and distribution of the NIH GenBank Sequence Database. NCBI distributes
GenBank sequence data by anonymous FTP, e-mail servers and other
network services. For more information, you may contact NCBI at the
e-mail address: [email protected] or by phone: 301-496-2475.
6.1 Registered Trademark Notice
GenBank (R) is a registered trademark of the U.S. Department of Health
and Human Services for the Genetic Sequence Data Bank.
6.2 Citing GenBank
If you have used GenBank in your research, we would appreciate it if
you would include a reference to GenBank in all publications related
to that research.
When citing data in GenBank, it is appropriate to give the sequence
name, primary accession number, and the publication in which the
sequence first appeared. If the data are unpublished, we urge you to
contact the group which submitted the data to GenBank to see if there
is a recent publication or if they have determined any revisions or
extensions of the data.
It is also appropriate to list a reference for GenBank itself. The
following publication, which describes the GenBank database, should
be cited:
Benson D.A., Karsch-Mizrachi I., Lipman D.J., Ostell J., Rapp B.A.,
Wheeler D.L. GenBank. Nucl. Acids Res. 28(1):15-18 (2000)
The following statement is an example of how you may cite GenBank
data. It cites the sequence, its primary accession number, the group
who determined the sequence, and GenBank. The numbers in parentheses
refer to the GenBank citation above and to the REFERENCE in the
GenBank sequence entry.
`We scanned the GenBank (1) database for sequence similarities and
found one sequence (2), GenBank accession number J01016, which showed
significant similarity...'
(1) Benson, D.A. et al. Nucl. Acids Res. 28(1):15-18 (2000)
(2) Nellen, W. and Gallwitz, D. J. Mol. Biol. 159, 1-18 (1982)
6.3 GenBank Distribution Formats and Media
Complete flat file releases of the GenBank database are available via
NCBI's anonymous ftp server:
ftp://ftp.ncbi.nih.gov
Each release is cumulative, incorporating all previous GenBank data.
No retrieval software is provided. GenBank distribution via CD-ROM
ceased as of GenBank Release 106.0 (April, 1998).
Mirrors of the GenBank FTP site at the NCBI are available from the
San Diego Supercomputer Center and the University of Indiana:
ftp://genbank.sdsc.edu/pub
ftp://bio-mirror.net/biomirror/genbank/
6.4 Other Methods of Accessing GenBank Data
Entrez is a molecular biology database system that presents an integrated
view of DNA and protein sequence data, 3D structure data, complete genomes,
and associated MEDLINE entries. The system is produced by the National
Center for Biotechnology Information (NCBI), and is available only via
the Internet (using the Web-Entrez and Network-Entrez applications).
Accessing Entrez is easy: if you have a World Wide Web browser, such as
Netscape or Internet-Explorer, simply point your browser to:
http://www.ncbi.nlm.nih.gov/
The Web version of Entrez has all the capabilities of the network version,
but with the visual style of the World Wide Web. If you prefer the "look and
feel" of Network-Entrez, you may download Network-Entrez from the NCBI's
FTP server:
ftp://ftp.ncbi.nih.gov/
Versions are available for PC/Windows, Macintosh and several Unix variants.
For information about Network-Entrez, Web-Entrez or any other NCBI
services, you may contact NCBI by e-mail at [email protected] or by
phone at 301-496-2475.
6.5 Request for Corrections and Comments
We welcome your suggestions for improvements to GenBank. We are
especially interested to learn of errors or inconsistencies in the
data. BankIt or Sequin can be used to submit revisions to previous
submissions. In addition, suggestions and corrections can be sent by
electronic mail to: [email protected]. Please be certain to
indicate the GenBank release number (e.g., Release 142.0) and the
primary accession number of the entry to which your comments apply; it
is helpful if you also give the entry name and the current contents of
any data field for which you are recommending a change.
6.6 Credits and Acknowledgments
Credits -
GenBank Release Coordination
Mark Cavanaugh
GenBank Submission Coordination
Ilene Mizrachi
GenBank Annotation Staff
Lori Black, Larissa Brown, Larry Chlumsky, Karen Clark, Irene Fang,
Linda Frisse, Michael Fetchko, Anjanette Johnston, William Klimke,
Pierre Ledoux, Richard McVeigh, Ilene Mizrachi, DeAnne Olsen Cravaritis,
Chris O'Sullivan, Leigh Riley, Gert Roosen, MJ Rosovitz, Susan Schafer,
Suh-suh Wang, and Linda Yankie
Data Management and Preparation
Vladimir Alekseyev, Serge Bazhin, Anton Butanaev, Mark Cavanaugh,
Hsiu-Chuan Chen, Olga Cherenkov, Jonathan Kans, Michael Kimelman,
Jim Ostell, Karl Sirotkin, Vladimir Soussov, Elena Starchenko,
Hanzhen Sun, Tatiana Tatusova, Carolyn Tolstoshev, Jane Weisemann,
Eugene Yaschenko
Database Administration
Slava Khotomliansky, Joe Pepersack, Tony Stearman
User Support
Medha Bhagwat, Peter Cooper, Susan Dombrowski, Andrei Gabrielian
Renata Geer, Scott McGinnis, Donna Messersmith, Rana Morris, Vyvy Pham,
Monica Romiti, Eric Sayers, Tao Tao, David Wheeler
Project Direction
David Lipman
Acknowledgments -
Contractor support for GenBank production and distribution has been
provided by Management Systems Designers, Inc., ComputerCraft Corporation,
and The KEVRIC Company, Inc.
6.7 Disclaimer
The United States Government makes no representations or warranties
regarding the content or accuracy of the information. The United States
Government also makes no representations or warranties of merchantability
or fitness for a particular purpose or that the use of the sequences will
not infringe any patent, copyright, trademark, or other rights. The
United States Government accepts no responsibility for any consequence
of the receipt or use of the information.
For additional information about GenBank releases, please contact
NCBI by e-mail at [email protected], by phone at (301) 496-2475,
or by mail at:
GenBank
National Library of Medicine
Bldg. 38A Rm. 8N-809
8600 Rockville Pike
Bethesda, MD 20894
FAX: (301) 480-9241
