Release Notes For GenBank Release 134
GBREL.TXT Genetic Sequence Data Bank
February 15 2003
NCBI-GenBank Flat File Release 134.00
Distribution Release Notes
23035823 loci, 29358082791 bases, from 23035823 reported sequences
This document describes the format and content of the flat files that
comprise releases of the GenBank 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
==========================================================================
TABLE OF CONTENTS
==========================================================================
1. INTRODUCTION
1.1 Release 134.0
1.2 Cutoff Date
1.3 Important Changes in Release 134.0
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
==========================================================================
1. INTRODUCTION
1.1 Release 134.0
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 134.0 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, 134.0, incorporates data available to the collaborating
databases as of February 10, 2003. For more recent data, users are advised to:
o Download the GenBank Update files by anonymous FTP to 'ftp.ncbi.nih.gov':
ftp://ftp.ncbi.nih.gov/ncbi-asn1 (ASN.1 format)
ftp://ftp.ncbi.nih.gov/genbank (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 (entire releases,
the GenBank Cumulative Update, etc) 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 134.0
1.3.1 Organizational changes
The total number of sequence data files increased by 10 with this release:
- the EST division is now comprised of 240 files (+5)
- the GSS division is now comprised of 66 files (+3)
- the HTC division is now comprised of 4 files (+1)
- the HTG division is now comprised of 58 files (+1)
1.3.2 * * Cumulative GenBank Update Products Discontinued * *
As of GenBank Release 134.0, the cumulative GenBank Update (GBCU)
products have been discontinued:
ftp://ftp.ncbi.nih.gov/ncbi-asn1/daily/gbcu.aso.gz
ftp://ftp.ncbi.nih.gov/genbank/daily/gbcu.flat.gz
ftp://ftp.ncbi.nih.gov/genbank/daily/gbcu.fsa_nt.gz
ftp://ftp.ncbi.nih.gov/genbank/daily/gbcu.gnp.gz
ftp://ftp.ncbi.nih.gov/genbank/daily/gbcu.qscore.gz
ftp://ftp.ncbi.nih.gov/genbank/daily/gpcu.fsa.gz
In the eight weeks between typical GenBank Releases, it was not uncommon
for GBCU products to approach 20% of the total database size. The flatfile
version, for example, reached sizes in excess of 17 GB in late 2002.
From a user perspective, repeatedly obtaining and processing such a
large update product makes inefficient use of both bandwidth and local
resources, compared to the much smaller incremental GbUpdate products.
And in order to reliably generate the GBCU in the face of such explosive
growth, NCBI would have to invest significant resources to increase the
performance of a large body of software.
Given these factors, plus the questionable value of an "update" product,
generated daily, and approaching 20GB in size, NCBI has discontinued
support for the GBCU products.
However, as an aid to those users who may not yet have completed
transitioning to the use of incremental update products, GBCU files
will continue to be generated, on an _unsupported_ basis, for approximately
three more weeks. After that time, the GBCU files will be removed from
the NCBI FTP site.
1.3.3 Third-Party Annotation Data Collection
Pursuant to agreements made at their 2002 Collaborative Meeting,
DDBJ/EMBL/GenBank have undertaken the collection of a new class of
sequence data : Third-Party Annotation (TPA).
The TPA data-collection complements the existing DDBJ/EMBL/GenBank
comprehensive database of primary nucleotide sequences, which typically
result from direct sequencing of cDNAs, ESTs, genomic DNAs, etc.
'Primary data' are defined to be data for which the submitting group has
done the sequencing and annotation, and hence, as owner of the data,
has privileges to update/correct the associated sequence records. In
contrast, non-primary (TPA) sequences are defined as sequences which:
a) consist exclusively of sequence data from one, or several,
previously-existing primary entries owned by other groups, or
b) consist of a mixture of previously-existing primary entries,
some owned by the TPA submittor and the rest by one or more other
groups
Complete details regarding TPA sequence submission can be found
at the NCBI website:
http://www.ncbi.nlm.nih.gov/Genbank/tpa.html
TPA categories and requirements
-------------------------------
Users can submit new annotation of single sequences or assemblies
of sequences that are owned by other groups to the TPA data
collection.
The primary sequences must be available in the DDBJ/EMBL/GenBank
databases, and submitters to the TPA database must provide the
accession numbers of the primary sequences in their TPA submission.
TPA sequences based on primary data available only in proprietary
databases are not accepted.
Some examples of data submissions accepted for TPA include:
1. analysis and re-annotation of DDBJ/EMBL/GenBank sequences
owned by other groups
2. gap-filling, in which a TPA submittor might utilize HTG or
EST data to complete an otherwise incomplete sequence
3. TPA sequences based on NCBI/Ensembl trace archive data
4. TPA sequences based on Whole Genome Shotgun (WGS) sequences
Sequences based on primary data from multiple organisms are not
accepted.
Sequences will not be accepted for TPA in lieu of an update to
primary records. A submittor who owns a primary record is expected
to update that record as new sequence is determined, or sequencing
ambiguities/errors are resolved.
Any newly-determined sequence data that is to be part of a TPA
record must first be submitted as a new primary sequence to
DDBJ/EMBL/GenBank.
The TPA dataset is intended to present sequence data and annotation
in support of actual biological discoveries that are published in
the scientific literature, without requiring that the sequence be
determined by the authors/submitters.
In order to assure that the sequence annotation is of high quality,
it is required that TPA records be associated with a study published
in a peer-reviewed journal before the data is released to the public.
TPA records include a mandatory 'PRIMARY' block, which documents the
relationships between spans of the TPA sequence and the primary
(non-TPA) sequences that contributed to it. The elements of the
PRIMARY block are:
a) TPA-SPAN base span on TPA sequence
b) PRIMARY_IDENTIFIER acc.version of contributing sequence(s)
c) PRIMARY_SPAN base span on contributing primary sequence
d) COMP 'c' is used to indicate that contributing
sequence is originating from complementary
strand in primary sequence entry
Example:
TPA_SPAN PRIMARY_IDENTIFIER PRIMARY_SPAN COMP
1-426 AC004528.1 18665-19090
427-526 AC001234.2 1-100 c
TPA data products
-----------------
TPA update products became available at the NCBI FTP site on Friday,
January 31, 2003. Daily, incremental update files for all new/updated
TPA records are located in:
ftp://ftp.ncbi.nih.gov/tpa/updates
TPA updates have filename prefixes of:
tpa_upd.YYYY.MMDD.
Filename suffixes for these updates are:
.bbs : binary Bioseq-set (ASN.1)
.gbff : GenBank flatfile
.gnp : GenPept flatfile
.fsa_nt : Nucleotide FASTA
.fsa_aa : Protein FASTA
We do not expect to generate complete releases (similar to GenBank
releases) for TPA until the volume of TPA records has substantially
increased. Until that time, a set of cumulative TPA update files
containing all TPA records is available in:
ftp://ftp.ncbi.nih.gov/tpa/release
Cumulative TPA update files have filename prefixes of:
tpa_cu.
and utilize the same filename suffixes that are listed above. Note
that the cumulative TPA products will be *discontinued* once TPA
releases are being built.
1.3.4 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 of nine
GSS flatfiles in Release 134.0. Consider the gbgss56.seq file:
GBGSS1.SEQ Genetic Sequence Data Bank
February 15 2003
NCBI-GenBank Flat File Release 134.0
GSS Sequences (Part 1)
88066 loci, 66600405 bases, from 88066 reported sequences
Here, the filename and part number in the header is "1", though the file
has been renamed as "56" 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 /mol_type qualifier
As of the April 2003 GenBank Release (134.0), a new source feature
qualifier called /mol_type will begin to be used for source features.
This qualifier will be used to indicate the in-vivo biological state
of the sequence presented in a database record.
The preliminary definition for /segment is :
Qualifier /mol_type=
Definition in vivo molecule type
Value format "text"
Example /mol_type="genomic DNA",
Comment text limited to "genomic DNA", "genomic RNA", "mRNA" (incl EST),
"tRNA", "rRNA", "snoRNA", "snRNA", "scRNA", "pre-mRNA",
"other RNA" (incl. synthetic), "other DNA" (incl. synthetic),
"unassigned DNA" (incl. unknown),"unassigned RNA" (incl. unknown)
In-vivo molecule type information is already presented on the LOCUS
line of the GenBank flatfile format. However, introducing /mol_type
in the Feature Table will make the exchange of this information among
DDBJ, EMBL, and GenBank more complete and accurate.
NOTE: /mol_type will eventually be a mandatory qualifier for the source
feature, probably by June 2003.
1.4.2 New /segment qualifier
As of the April 2003 GenBank Release (134.0), a new source feature
qualifier called /segment will begin to be used for source features.
In the absence of a more suitable way to annotate viral segments, this
information had either not been included in database entries, or had been
annotated incorrectly (e.g. using /chromosome, /map etc). This new
qualifier addresses that lack.
The preliminary definition for /segment is :
Qualifier /segment=
Definition name of viral or phage segment sequenced
Value format "text"
Example /segment="6"
1.4.3 New /locus_tag qualifier
As of the April 2003 GenBank Release (134.0), a new source feature
qualifier called /locus_tag will begin to be used.
Many complete-genome sequencing projects use solely computational
methods to predict coding regions and genes. The /locus_tag qualifier
provides a method for identifying and tracking the results of such
computations, without utilizing existing qualifiers such as /gene .
These 'locus tags' are systematically assigned, and do not necessarily
reflect gene name/symbol conventions in experimental literature. Hence
the introduction of this new qualifier.
The preliminary definition for /locus_tag is :
Qualifier: /locus_tag
Definition: feature tag assigned for tracking purposes
Value Format: "text" (single token)
Example: /locus_tag="RSc0382"
/locus_tag="YPO0002"
Comment: /locus_tag can be used with any feature where /gene
is valid;
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 464 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
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. gbjou.idx - Index of the entries according to journal citation.
25. gbgen.idx - Index of the entries according to gene names.
26. gbsec.idx - Index of the entries according to secondary accession number.
27. gbpri1.seq - Primate sequence entries, part 1.
28. gbpri2.seq - Primate sequence entries, part 2.
29. gbpri3.seq - Primate sequence entries, part 3.
30. gbpri4.seq - Primate sequence entries, part 4.
31. gbpri5.seq - Primate sequence entries, part 5.
32. gbpri6.seq - Primate sequence entries, part 6.
33. gbpri7.seq - Primate sequence entries, part 7.
34. gbpri8.seq - Primate sequence entries, part 8.
35. gbpri9.seq - Primate sequence entries, part 9.
36. gbpri10.seq - Primate sequence entries, part 10.
37. gbpri11.seq - Primate sequence entries, part 11.
38. gbpri12.seq - Primate sequence entries, part 12.
39. gbpri13.seq - Primate sequence entries, part 13.
40. gbpri14.seq - Primate sequence entries, part 14.
41. gbpri15.seq - Primate sequence entries, part 15.
42. gbpri16.seq - Primate sequence entries, part 16.
43. gbpri17.seq - Primate sequence entries, part 17.
44. gbpri18.seq - Primate sequence entries, part 18.
45. gbpri19.seq - Primate sequence entries, part 19.
46. gbpri20.seq - Primate sequence entries, part 20.
47. gbpri21.seq - Primate sequence entries, part 21.
48. gbpri22.seq - Primate sequence entries, part 22.
49. gbpri23.seq - Primate sequence entries, part 23.
50. gbpri24.seq - Primate sequence entries, part 24.
51. gbrod1.seq - Rodent sequence entries, part 1.
52. gbrod2.seq - Rodent sequence entries, part 2.
53. gbrod3.seq - Rodent sequence entries, part 3.
54. gbrod4.seq - Rodent sequence entries, part 4.
55. gbrod5.seq - Rodent sequence entries, part 5.
56. gbrod6.seq - Rodent sequence entries, part 6.
57. gbmam.seq - Other mammalian sequence entries.
58. gbvrt1.seq - Other vertebrate sequence entries, part 1.
59. gbvrt2.seq - Other vertebrate sequence entries, part 2.
60. gbinv1.seq - Invertebrate sequence entries, part 1.
61. gbinv2.seq - Invertebrate sequence entries, part 2.
62. gbinv3.seq - Invertebrate sequence entries, part 3.
63. gbinv4.seq - Invertebrate sequence entries, part 4.
64. gbinv5.seq - Invertebrate sequence entries, part 5.
65. gbpln1.seq - Plant sequence entries (including fungi and algae), part 1.
66. gbpln2.seq - Plant sequence entries (including fungi and algae), part 2.
67. gbpln3.seq - Plant sequence entries (including fungi and algae), part 3.
68. gbpln4.seq - Plant sequence entries (including fungi and algae), part 4.
69. gbpln5.seq - Plant sequence entries (including fungi and algae), part 5.
70. gbpln6.seq - Plant sequence entries (including fungi and algae), part 6.
71. gbpln7.seq - Plant sequence entries (including fungi and algae), part 7.
72. gbbct1.seq - Bacterial sequence entries, part 1.
73. gbbct2.seq - Bacterial sequence entries, part 2.
74. gbbct3.seq - Bacterial sequence entries, part 3.
75. gbbct4.seq - Bacterial sequence entries, part 4.
76. gbbct5.seq - Bacterial sequence entries, part 5.
77. gbbct6.seq - Bacterial sequence entries, part 6.
78. gbvrl1.seq - Viral sequence entries, part 1.
79. gbvrl2.seq - Viral sequence entries, part 2.
80. gbvrl3.seq - Viral sequence entries, part 3.
81. gbphg.seq - Phage sequence entries.
82. gbsyn.seq - Synthetic and chimeric sequence entries.
83. gbuna.seq - Unannotated sequence entries.
84. gbest1.seq - EST (expressed sequence tag) sequence entries, part 1.
85. gbest2.seq - EST (expressed sequence tag) sequence entries, part 2.
86. gbest3.seq - EST (expressed sequence tag) sequence entries, part 3.
87. gbest4.seq - EST (expressed sequence tag) sequence entries, part 4.
88. gbest5.seq - EST (expressed sequence tag) sequence entries, part 5.
89. gbest6.seq - EST (expressed sequence tag) sequence entries, part 6.
90. gbest7.seq - EST (expressed sequence tag) sequence entries, part 7.
91. gbest8.seq - EST (expressed sequence tag) sequence entries, part 8.
92. gbest9.seq - EST (expressed sequence tag) sequence entries, part 9.
93. gbest10.seq - EST (expressed sequence tag) sequence entries, part 10.
94. gbest11.seq - EST (expressed sequence tag) sequence entries, part 11.
95. gbest12.seq - EST (expressed sequence tag) sequence entries, part 12.
96. gbest13.seq - EST (expressed sequence tag) sequence entries, part 13.
97. gbest14.seq - EST (expressed sequence tag) sequence entries, part 14.
98. gbest15.seq - EST (expressed sequence tag) sequence entries, part 15.
99. gbest16.seq - EST (expressed sequence tag) sequence entries, part 16.
100. gbest17.seq - EST (expressed sequence tag) sequence entries, part 17.
101. gbest18.seq - EST (expressed sequence tag) sequence entries, part 18.
102. gbest19.seq - EST (expressed sequence tag) sequence entries, part 19.
103. gbest20.seq - EST (expressed sequence tag) sequence entries, part 20.
104. gbest21.seq - EST (expressed sequence tag) sequence entries, part 21.
105. gbest22.seq - EST (expressed sequence tag) sequence entries, part 22.
106. gbest23.seq - EST (expressed sequence tag) sequence entries, part 23.
107. gbest24.seq - EST (expressed sequence tag) sequence entries, part 24.
108. gbest25.seq - EST (expressed sequence tag) sequence entries, part 25.
109. gbest26.seq - EST (expressed sequence tag) sequence entries, part 26.
110. gbest27.seq - EST (expressed sequence tag) sequence entries, part 27.
111. gbest28.seq - EST (expressed sequence tag) sequence entries, part 28.
112. gbest29.seq - EST (expressed sequence tag) sequence entries, part 29.
113. gbest30.seq - EST (expressed sequence tag) sequence entries, part 30.
114. gbest31.seq - EST (expressed sequence tag) sequence entries, part 31.
115. gbest32.seq - EST (expressed sequence tag) sequence entries, part 32.
116. gbest33.seq - EST (expressed sequence tag) sequence entries, part 33.
117. gbest34.seq - EST (expressed sequence tag) sequence entries, part 34.
118. gbest35.seq - EST (expressed sequence tag) sequence entries, part 35.
119. gbest36.seq - EST (expressed sequence tag) sequence entries, part 36.
120. gbest37.seq - EST (expressed sequence tag) sequence entries, part 37.
121. gbest38.seq - EST (expressed sequence tag) sequence entries, part 38.
122. gbest39.seq - EST (expressed sequence tag) sequence entries, part 39.
123. gbest40.seq - EST (expressed sequence tag) sequence entries, part 40.
124. gbest41.seq - EST (expressed sequence tag) sequence entries, part 41.
125. gbest42.seq - EST (expressed sequence tag) sequence entries, part 42.
126. gbest43.seq - EST (expressed sequence tag) sequence entries, part 43.
127. gbest44.seq - EST (expressed sequence tag) sequence entries, part 44.
128. gbest45.seq - EST (expressed sequence tag) sequence entries, part 45.
129. gbest46.seq - EST (expressed sequence tag) sequence entries, part 46.
130. gbest47.seq - EST (expressed sequence tag) sequence entries, part 47.
131. gbest48.seq - EST (expressed sequence tag) sequence entries, part 48.
132. gbest49.seq - EST (expressed sequence tag) sequence entries, part 49.
133. gbest50.seq - EST (expressed sequence tag) sequence entries, part 50.
134. gbest51.seq - EST (expressed sequence tag) sequence entries, part 51.
135. gbest52.seq - EST (expressed sequence tag) sequence entries, part 52.
136. gbest53.seq - EST (expressed sequence tag) sequence entries, part 53.
137. gbest54.seq - EST (expressed sequence tag) sequence entries, part 54.
138. gbest55.seq - EST (expressed sequence tag) sequence entries, part 55.
139. gbest56.seq - EST (expressed sequence tag) sequence entries, part 56.
140. gbest57.seq - EST (expressed sequence tag) sequence entries, part 57.
141. gbest58.seq - EST (expressed sequence tag) sequence entries, part 58.
142. gbest59.seq - EST (expressed sequence tag) sequence entries, part 59.
143. gbest60.seq - EST (expressed sequence tag) sequence entries, part 60.
144. gbest61.seq - EST (expressed sequence tag) sequence entries, part 61.
145. gbest62.seq - EST (expressed sequence tag) sequence entries, part 62.
146. gbest63.seq - EST (expressed sequence tag) sequence entries, part 63.
147. gbest64.seq - EST (expressed sequence tag) sequence entries, part 64.
148. gbest65.seq - EST (expressed sequence tag) sequence entries, part 65.
149. gbest66.seq - EST (expressed sequence tag) sequence entries, part 66.
150. gbest67.seq - EST (expressed sequence tag) sequence entries, part 67.
151. gbest68.seq - EST (expressed sequence tag) sequence entries, part 68.
152. gbest69.seq - EST (expressed sequence tag) sequence entries, part 69.
153. gbest70.seq - EST (expressed sequence tag) sequence entries, part 70.
154. gbest71.seq - EST (expressed sequence tag) sequence entries, part 71.
155. gbest72.seq - EST (expressed sequence tag) sequence entries, part 72.
156. gbest73.seq - EST (expressed sequence tag) sequence entries, part 73.
157. gbest74.seq - EST (expressed sequence tag) sequence entries, part 74.
158. gbest75.seq - EST (expressed sequence tag) sequence entries, part 75.
159. gbest76.seq - EST (expressed sequence tag) sequence entries, part 76.
160. gbest77.seq - EST (expressed sequence tag) sequence entries, part 77.
161. gbest78.seq - EST (expressed sequence tag) sequence entries, part 78.
162. gbest79.seq - EST (expressed sequence tag) sequence entries, part 79.
163. gbest80.seq - EST (expressed sequence tag) sequence entries, part 80.
164. gbest81.seq - EST (expressed sequence tag) sequence entries, part 81.
165. gbest82.seq - EST (expressed sequence tag) sequence entries, part 82.
166. gbest83.seq - EST (expressed sequence tag) sequence entries, part 83.
167. gbest84.seq - EST (expressed sequence tag) sequence entries, part 84.
168. gbest85.seq - EST (expressed sequence tag) sequence entries, part 85.
169. gbest86.seq - EST (expressed sequence tag) sequence entries, part 86.
170. gbest87.seq - EST (expressed sequence tag) sequence entries, part 87.
171. gbest88.seq - EST (expressed sequence tag) sequence entries, part 88.
172. gbest89.seq - EST (expressed sequence tag) sequence entries, part 89
173. gbest90.seq - EST (expressed sequence tag) sequence entries, part 90.
174. gbest91.seq - EST (expressed sequence tag) sequence entries, part 91.
175. gbest92.seq - EST (expressed sequence tag) sequence entries, part 92.
176. gbest93.seq - EST (expressed sequence tag) sequence entries, part 93.
177. gbest94.seq - EST (expressed sequence tag) sequence entries, part 94.
178. gbest95.seq - EST (expressed sequence tag) sequence entries, part 95.
179. gbest96.seq - EST (expressed sequence tag) sequence entries, part 96.
180. gbest97.seq - EST (expressed sequence tag) sequence entries, part 97.
181. gbest98.seq - EST (expressed sequence tag) sequence entries, part 98.
182. gbest99.seq - EST (expressed sequence tag) sequence entries, part 99.
183. gbest100.seq - EST (expressed sequence tag) sequence entries, part 100.
184. gbest101.seq - EST (expressed sequence tag) sequence entries, part 101.
185. gbest102.seq - EST (expressed sequence tag) sequence entries, part 102.
186. gbest103.seq - EST (expressed sequence tag) sequence entries, part 103.
187. gbest104.seq - EST (expressed sequence tag) sequence entries, part 104.
188. gbest105.seq - EST (expressed sequence tag) sequence entries, part 105.
189. gbest106.seq - EST (expressed sequence tag) sequence entries, part 106.
190. gbest107.seq - EST (expressed sequence tag) sequence entries, part 107.
191. gbest108.seq - EST (expressed sequence tag) sequence entries, part 108.
192. gbest109.seq - EST (expressed sequence tag) sequence entries, part 109.
193. gbest110.seq - EST (expressed sequence tag) sequence entries, part 110.
194. gbest111.seq - EST (expressed sequence tag) sequence entries, part 111.
195. gbest112.seq - EST (expressed sequence tag) sequence entries, part 112.
196. gbest113.seq - EST (expressed sequence tag) sequence entries, part 113.
197. gbest114.seq - EST (expressed sequence tag) sequence entries, part 114.
198. gbest115.seq - EST (expressed sequence tag) sequence entries, part 115.
199. gbest116.seq - EST (expressed sequence tag) sequence entries, part 116.
200. gbest117.seq - EST (expressed sequence tag) sequence entries, part 117.
201. gbest118.seq - EST (expressed sequence tag) sequence entries, part 118.
202. gbest119.seq - EST (expressed sequence tag) sequence entries, part 119.
203. gbest120.seq - EST (expressed sequence tag) sequence entries, part 120.
204. gbest121.seq - EST (expressed sequence tag) sequence entries, part 121.
205. gbest122.seq - EST (expressed sequence tag) sequence entries, part 122.
206. gbest123.seq - EST (expressed sequence tag) sequence entries, part 123.
207. gbest124.seq - EST (expressed sequence tag) sequence entries, part 124.
208. gbest125.seq - EST (expressed sequence tag) sequence entries, part 125.
209. gbest126.seq - EST (expressed sequence tag) sequence entries, part 126.
210. gbest127.seq - EST (expressed sequence tag) sequence entries, part 127.
211. gbest128.seq - EST (expressed sequence tag) sequence entries, part 128.
212. gbest129.seq - EST (expressed sequence tag) sequence entries, part 129.
213. gbest130.seq - EST (expressed sequence tag) sequence entries, part 130.
214. gbest131.seq - EST (expressed sequence tag) sequence entries, part 131.
215. gbest132.seq - EST (expressed sequence tag) sequence entries, part 132.
216. gbest133.seq - EST (expressed sequence tag) sequence entries, part 133.
217. gbest134.seq - EST (expressed sequence tag) sequence entries, part 134.
218. gbest135.seq - EST (expressed sequence tag) sequence entries, part 135.
219. gbest136.seq - EST (expressed sequence tag) sequence entries, part 136.
220. gbest137.seq - EST (expressed sequence tag) sequence entries, part 137.
221. gbest138.seq - EST (expressed sequence tag) sequence entries, part 138.
222. gbest139.seq - EST (expressed sequence tag) sequence entries, part 139.
223. gbest140.seq - EST (expressed sequence tag) sequence entries, part 140.
224. gbest141.seq - EST (expressed sequence tag) sequence entries, part 141.
225. gbest142.seq - EST (expressed sequence tag) sequence entries, part 142.
226. gbest143.seq - EST (expressed sequence tag) sequence entries, part 143.
227. gbest144.seq - EST (expressed sequence tag) sequence entries, part 144.
228. gbest145.seq - EST (expressed sequence tag) sequence entries, part 145.
229. gbest146.seq - EST (expressed sequence tag) sequence entries, part 146.
230. gbest147.seq - EST (expressed sequence tag) sequence entries, part 147.
231. gbest148.seq - EST (expressed sequence tag) sequence entries, part 148.
232. gbest149.seq - EST (expressed sequence tag) sequence entries, part 149.
233. gbest150.seq - EST (expressed sequence tag) sequence entries, part 150.
234. gbest151.seq - EST (expressed sequence tag) sequence entries, part 151.
235. gbest152.seq - EST (expressed sequence tag) sequence entries, part 152.
236. gbest153.seq - EST (expressed sequence tag) sequence entries, part 153.
237. gbest154.seq - EST (expressed sequence tag) sequence entries, part 154.
238. gbest155.seq - EST (expressed sequence tag) sequence entries, part 155.
239. gbest156.seq - EST (expressed sequence tag) sequence entries, part 156.
240. gbest157.seq - EST (expressed sequence tag) sequence entries, part 157.
241. gbest158.seq - EST (expressed sequence tag) sequence entries, part 158.
242. gbest159.seq - EST (expressed sequence tag) sequence entries, part 159.
243. gbest160.seq - EST (expressed sequence tag) sequence entries, part 160.
244. gbest161.seq - EST (expressed sequence tag) sequence entries, part 161.
245. gbest162.seq - EST (expressed sequence tag) sequence entries, part 162.
246. gbest163.seq - EST (expressed sequence tag) sequence entries, part 163.
247. gbest164.seq - EST (expressed sequence tag) sequence entries, part 164.
248. gbest165.seq - EST (expressed sequence tag) sequence entries, part 165.
249. gbest166.seq - EST (expressed sequence tag) sequence entries, part 166.
250. gbest167.seq - EST (expressed sequence tag) sequence entries, part 167.
251. gbest168.seq - EST (expressed sequence tag) sequence entries, part 168.
252. gbest169.seq - EST (expressed sequence tag) sequence entries, part 169.
253. gbest170.seq - EST (expressed sequence tag) sequence entries, part 170.
254. gbest171.seq - EST (expressed sequence tag) sequence entries, part 171.
255. gbest172.seq - EST (expressed sequence tag) sequence entries, part 172.
256. gbest173.seq - EST (expressed sequence tag) sequence entries, part 173.
257. gbest174.seq - EST (expressed sequence tag) sequence entries, part 174.
258. gbest175.seq - EST (expressed sequence tag) sequence entries, part 175.
259. gbest176.seq - EST (expressed sequence tag) sequence entries, part 176.
260. gbest177.seq - EST (expressed sequence tag) sequence entries, part 177.
261. gbest178.seq - EST (expressed sequence tag) sequence entries, part 178.
262. gbest179.seq - EST (expressed sequence tag) sequence entries, part 179.
263. gbest180.seq - EST (expressed sequence tag) sequence entries, part 180.
264. gbest181.seq - EST (expressed sequence tag) sequence entries, part 181.
265. gbest182.seq - EST (expressed sequence tag) sequence entries, part 182.
266. gbest183.seq - EST (expressed sequence tag) sequence entries, part 183.
267. gbest184.seq - EST (expressed sequence tag) sequence entries, part 184.
268. gbest185.seq - EST (expressed sequence tag) sequence entries, part 185.
269. gbest186.seq - EST (expressed sequence tag) sequence entries, part 186.
270. gbest187.seq - EST (expressed sequence tag) sequence entries, part 187.
271. gbest188.seq - EST (expressed sequence tag) sequence entries, part 188.
272. gbest189.seq - EST (expressed sequence tag) sequence entries, part 189.
273. gbest190.seq - EST (expressed sequence tag) sequence entries, part 190.
274. gbest191.seq - EST (expressed sequence tag) sequence entries, part 191.
275. gbest192.seq - EST (expressed sequence tag) sequence entries, part 192.
276. gbest193.seq - EST (expressed sequence tag) sequence entries, part 193.
277. gbest194.seq - EST (expressed sequence tag) sequence entries, part 194.
278. gbest195.seq - EST (expressed sequence tag) sequence entries, part 195.
279. gbest196.seq - EST (expressed sequence tag) sequence entries, part 196.
280. gbest197.seq - EST (expressed sequence tag) sequence entries, part 197.
281. gbest198.seq - EST (expressed sequence tag) sequence entries, part 198.
282. gbest199.seq - EST (expressed sequence tag) sequence entries, part 199.
283. gbest200.seq - EST (expressed sequence tag) sequence entries, part 200.
284. gbest201.seq - EST (expressed sequence tag) sequence entries, part 201.
285. gbest202.seq - EST (expressed sequence tag) sequence entries, part 202.
286. gbest203.seq - EST (expressed sequence tag) sequence entries, part 203.
287. gbest204.seq - EST (expressed sequence tag) sequence entries, part 204.
288. gbest205.seq - EST (expressed sequence tag) sequence entries, part 205.
289. gbest206.seq - EST (expressed sequence tag) sequence entries, part 206.
290. gbest207.seq - EST (expressed sequence tag) sequence entries, part 207.
291. gbest208.seq - EST (expressed sequence tag) sequence entries, part 208.
292. gbest209.seq - EST (expressed sequence tag) sequence entries, part 209.
293. gbest210.seq - EST (expressed sequence tag) sequence entries, part 210.
294. gbest211.seq - EST (expressed sequence tag) sequence entries, part 211.
295. gbest212.seq - EST (expressed sequence tag) sequence entries, part 212.
296. gbest213.seq - EST (expressed sequence tag) sequence entries, part 213.
297. gbest214.seq - EST (expressed sequence tag) sequence entries, part 214.
298. gbest215.seq - EST (expressed sequence tag) sequence entries, part 215.
299. gbest216.seq - EST (expressed sequence tag) sequence entries, part 216.
300. gbest217.seq - EST (expressed sequence tag) sequence entries, part 217.
301. gbest218.seq - EST (expressed sequence tag) sequence entries, part 218.
302. gbest219.seq - EST (expressed sequence tag) sequence entries, part 219.
303. gbest220.seq - EST (expressed sequence tag) sequence entries, part 220.
304. gbest221.seq - EST (expressed sequence tag) sequence entries, part 221.
305. gbest222.seq - EST (expressed sequence tag) sequence entries, part 222.
306. gbest223.seq - EST (expressed sequence tag) sequence entries, part 223.
307. gbest224.seq - EST (expressed sequence tag) sequence entries, part 224.
308. gbest225.seq - EST (expressed sequence tag) sequence entries, part 225.
309. gbest226.seq - EST (expressed sequence tag) sequence entries, part 226.
310. gbest227.seq - EST (expressed sequence tag) sequence entries, part 227.
311. gbest228.seq - EST (expressed sequence tag) sequence entries, part 228.
312. gbest229.seq - EST (expressed sequence tag) sequence entries, part 229.
313. gbest230.seq - EST (expressed sequence tag) sequence entries, part 230.
314. gbest231.seq - EST (expressed sequence tag) sequence entries, part 231.
315. gbest232.seq - EST (expressed sequence tag) sequence entries, part 232.
316. gbest233.seq - EST (expressed sequence tag) sequence entries, part 233.
317. gbest234.seq - EST (expressed sequence tag) sequence entries, part 234.
318. gbest235.seq - EST (expressed sequence tag) sequence entries, part 235.
319. gbest236.seq - EST (expressed sequence tag) sequence entries, part 236.
320. gbest237.seq - EST (expressed sequence tag) sequence entries, part 237.
321. gbest238.seq - EST (expressed sequence tag) sequence entries, part 238.
322. gbest239.seq - EST (expressed sequence tag) sequence entries, part 239.
323. gbest240.seq - EST (expressed sequence tag) sequence entries, part 240.
324. gbpat1.seq - Patent sequence entries, part 1.
325. gbpat2.seq - Patent sequence entries, part 2.
326. gbpat3.seq - Patent sequence entries, part 3.
327. gbpat4.seq - Patent sequence entries, part 4.
328. gbpat5.seq - Patent sequence entries, part 5.
329. gbpat6.seq - Patent sequence entries, part 6.
330. gbpat7.seq - Patent sequence entries, part 7.
331. gbsts1.seq - STS (sequence tagged site) sequence entries, part 1.
332. gbsts2.seq - STS (sequence tagged site) sequence entries, part 2.
333. gbgss1.seq - GSS (genome survey sequence) sequence entries, part 1.
334. gbgss2.seq - GSS (genome survey sequence) sequence entries, part 2.
335. gbgss3.seq - GSS (genome survey sequence) sequence entries, part 3.
336. gbgss4.seq - GSS (genome survey sequence) sequence entries, part 4.
337. gbgss5.seq - GSS (genome survey sequence) sequence entries, part 5.
338. gbgss6.seq - GSS (genome survey sequence) sequence entries, part 6.
339. gbgss7.seq - GSS (genome survey sequence) sequence entries, part 7.
340. gbgss8.seq - GSS (genome survey sequence) sequence entries, part 8.
341. gbgss9.seq - GSS (genome survey sequence) sequence entries, part 9.
342. gbgss10.seq - GSS (genome survey sequence) sequence entries, part 10.
343. gbgss11.seq - GSS (genome survey sequence) sequence entries, part 11.
344. gbgss12.seq - GSS (genome survey sequence) sequence entries, part 12.
345. gbgss13.seq - GSS (genome survey sequence) sequence entries, part 13.
346. gbgss14.seq - GSS (genome survey sequence) sequence entries, part 14.
347. gbgss15.seq - GSS (genome survey sequence) sequence entries, part 15.
348. gbgss16.seq - GSS (genome survey sequence) sequence entries, part 16.
349. gbgss17.seq - GSS (genome survey sequence) sequence entries, part 17.
350. gbgss18.seq - GSS (genome survey sequence) sequence entries, part 18.
351. gbgss19.seq - GSS (genome survey sequence) sequence entries, part 19.
352. gbgss20.seq - GSS (genome survey sequence) sequence entries, part 20.
353. gbgss21.seq - GSS (genome survey sequence) sequence entries, part 21.
354. gbgss22.seq - GSS (genome survey sequence) sequence entries, part 22.
355. gbgss23.seq - GSS (genome survey sequence) sequence entries, part 23.
356. gbgss24.seq - GSS (genome survey sequence) sequence entries, part 24.
357. gbgss25.seq - GSS (genome survey sequence) sequence entries, part 25.
358. gbgss26.seq - GSS (genome survey sequence) sequence entries, part 26.
359. gbgss27.seq - GSS (genome survey sequence) sequence entries, part 27.
360. gbgss28.seq - GSS (genome survey sequence) sequence entries, part 28.
361. gbgss29.seq - GSS (genome survey sequence) sequence entries, part 29.
362. gbgss30.seq - GSS (genome survey sequence) sequence entries, part 30.
363. gbgss31.seq - GSS (genome survey sequence) sequence entries, part 31.
364. gbgss32.seq - GSS (genome survey sequence) sequence entries, part 32.
365. gbgss33.seq - GSS (genome survey sequence) sequence entries, part 33.
366. gbgss34.seq - GSS (genome survey sequence) sequence entries, part 34.
367. gbgss35.seq - GSS (genome survey sequence) sequence entries, part 35.
368. gbgss36.seq - GSS (genome survey sequence) sequence entries, part 36.
369. gbgss37.seq - GSS (genome survey sequence) sequence entries, part 37.
370. gbgss38.seq - GSS (genome survey sequence) sequence entries, part 38.
371. gbgss39.seq - GSS (genome survey sequence) sequence entries, part 39.
372. gbgss40.seq - GSS (genome survey sequence) sequence entries, part 40.
373. gbgss41.seq - GSS (genome survey sequence) sequence entries, part 41.
374. gbgss42.seq - GSS (genome survey sequence) sequence entries, part 42.
375. gbgss43.seq - GSS (genome survey sequence) sequence entries, part 43.
376. gbgss44.seq - GSS (genome survey sequence) sequence entries, part 44.
377. gbgss45.seq - GSS (genome survey sequence) sequence entries, part 45.
378. gbgss46.seq - GSS (genome survey sequence) sequence entries, part 46.
379. gbgss47.seq - GSS (genome survey sequence) sequence entries, part 47.
380. gbgss48.seq - GSS (genome survey sequence) sequence entries, part 48.
381. gbgss49.seq - GSS (genome survey sequence) sequence entries, part 49.
382. gbgss50.seq - GSS (genome survey sequence) sequence entries, part 50.
383. gbgss51.seq - GSS (genome survey sequence) sequence entries, part 51.
384. gbgss52.seq - GSS (genome survey sequence) sequence entries, part 52.
385. gbgss53.seq - GSS (genome survey sequence) sequence entries, part 53.
386. gbgss54.seq - GSS (genome survey sequence) sequence entries, part 54.
387. gbgss55.seq - GSS (genome survey sequence) sequence entries, part 55.
388. gbgss56.seq - GSS (genome survey sequence) sequence entries, part 56.
389. gbgss57.seq - GSS (genome survey sequence) sequence entries, part 57.
390. gbgss58.seq - GSS (genome survey sequence) sequence entries, part 58.
391. gbgss59.seq - GSS (genome survey sequence) sequence entries, part 59.
392. gbgss60.seq - GSS (genome survey sequence) sequence entries, part 60.
393. gbgss61.seq - GSS (genome survey sequence) sequence entries, part 61.
394. gbgss62.seq - GSS (genome survey sequence) sequence entries, part 62.
395. gbgss63.seq - GSS (genome survey sequence) sequence entries, part 63.
396. gbgss64.seq - GSS (genome survey sequence) sequence entries, part 64.
397. gbgss65.seq - GSS (genome survey sequence) sequence entries, part 65.
398. gbgss66.seq - GSS (genome survey sequence) sequence entries, part 66.
399. gbhtg1.seq - HTGS (high throughput genomic sequencing) sequence entries, part 1.
400. gbhtg2.seq - HTGS (high throughput genomic sequencing) sequence entries, part 2.
401. gbhtg3.seq - HTGS (high throughput genomic sequencing) sequence entries, part 3.
402. gbhtg4.seq - HTGS (high throughput genomic sequencing) sequence entries, part 4.
403. gbhtg5.seq - HTGS (high throughput genomic sequencing) sequence entries, part 5.
404. gbhtg6.seq - HTGS (high throughput genomic sequencing) sequence entries, part 6.
405. gbhtg7.seq - HTGS (high throughput genomic sequencing) sequence entries, part 7.
406. gbhtg8.seq - HTGS (high throughput genomic sequencing) sequence entries, part 8.
407. gbhtg9.seq - HTGS (high throughput genomic sequencing) sequence entries, part 9.
408. gbhtg10.seq - HTGS (high throughput genomic sequencing) sequence entries, part 10.
409. gbhtg11.seq - HTGS (high throughput genomic sequencing) sequence entries, part 11.
410. gbhtg12.seq - HTGS (high throughput genomic sequencing) sequence entries, part 12.
411. gbhtg13.seq - HTGS (high throughput genomic sequencing) sequence entries, part 13.
412. gbhtg14.seq - HTGS (high throughput genomic sequencing) sequence entries, part 14.
413. gbhtg15.seq - HTGS (high throughput genomic sequencing) sequence entries, part 15.
414. gbhtg16.seq - HTGS (high throughput genomic sequencing) sequence entries, part 16.
415. gbhtg17.seq - HTGS (high throughput genomic sequencing) sequence entries, part 17.
416. gbhtg18.seq - HTGS (high throughput genomic sequencing) sequence entries, part 18.
417. gbhtg19.seq - HTGS (high throughput genomic sequencing) sequence entries, part 19.
418. gbhtg20.seq - HTGS (high throughput genomic sequencing) sequence entries, part 20.
419. gbhtg21.seq - HTGS (high throughput genomic sequencing) sequence entries, part 21.
420. gbhtg22.seq - HTGS (high throughput genomic sequencing) sequence entries, part 22.
421. gbhtg23.seq - HTGS (high throughput genomic sequencing) sequence entries, part 23.
422. gbhtg24.seq - HTGS (high throughput genomic sequencing) sequence entries, part 24.
423. gbhtg25.seq - HTGS (high throughput genomic sequencing) sequence entries, part 25.
424. gbhtg26.seq - HTGS (high throughput genomic sequencing) sequence entries, part 26.
425. gbhtg27.seq - HTGS (high throughput genomic sequencing) sequence entries, part 27.
426. gbhtg28.seq - HTGS (high throughput genomic sequencing) sequence entries, part 28.
427. gbhtg29.seq - HTGS (high throughput genomic sequencing) sequence entries, part 29.
428. gbhtg30.seq - HTGS (high throughput genomic sequencing) sequence entries, part 30.
429. gbhtg31.seq - HTGS (high throughput genomic sequencing) sequence entries, part 31.
430. gbhtg32.seq - HTGS (high throughput genomic sequencing) sequence entries, part 32.
431. gbhtg33.seq - HTGS (high throughput genomic sequencing) sequence entries, part 33.
432. gbhtg34.seq - HTGS (high throughput genomic sequencing) sequence entries, part 34.
433. gbhtg35.seq - HTGS (high throughput genomic sequencing) sequence entries, part 35.
434. gbhtg36.seq - HTGS (high throughput genomic sequencing) sequence entries, part 36.
435. gbhtg37.seq - HTGS (high throughput genomic sequencing) sequence entries, part 37.
436. gbhtg38.seq - HTGS (high throughput genomic sequencing) sequence entries, part 38.
437. gbhtg39.seq - HTGS (high throughput genomic sequencing) sequence entries, part 39.
438. gbhtg40.seq - HTGS (high throughput genomic sequencing) sequence entries, part 40.
439. gbhtg41.seq - HTGS (high throughput genomic sequencing) sequence entries, part 41.
440. gbhtg42.seq - HTGS (high throughput genomic sequencing) sequence entries, part 42.
441. gbhtg43.seq - HTGS (high throughput genomic sequencing) sequence entries, part 43.
442. gbhtg44.seq - HTGS (high throughput genomic sequencing) sequence entries, part 44.
443. gbhtg45.seq - HTGS (high throughput genomic sequencing) sequence entries, part 45.
444. gbhtg46.seq - HTGS (high throughput genomic sequencing) sequence entries, part 46.
445. gbhtg47.seq - HTGS (high throughput genomic sequencing) sequence entries, part 47.
446. gbhtg48.seq - HTGS (high throughput genomic sequencing) sequence entries, part 48.
447. gbhtg49.seq - HTGS (high throughput genomic sequencing) sequence entries, part 49.
448. gbhtg50.seq - HTGS (high throughput genomic sequencing) sequence entries, part 50.
449. gbhtg51.seq - HTGS (high throughput genomic sequencing) sequence entries, part 51.
450. gbhtg52.seq - HTGS (high throughput genomic sequencing) sequence entries, part 52.
451. gbhtg53.seq - HTGS (high throughput genomic sequencing) sequence entries, part 53.
452. gbhtg54.seq - HTGS (high throughput genomic sequencing) sequence entries, part 54.
453. gbhtg55.seq - HTGS (high throughput genomic sequencing) sequence entries, part 55.
454. gbhtg56.seq - HTGS (high throughput genomic sequencing) sequence entries, part 56.
455. gbhtg57.seq - HTGS (high throughput genomic sequencing) sequence entries, part 57.
456. gbhtg58.seq - HTGS (high throughput genomic sequencing) sequence entries, part 58.
457. gbhtc1.seq - HTC (high throughput cDNA sequencing) entries, part 1.
458. gbhtc2.seq - HTC (high throughput cDNA sequencing) entries, part 2.
459. gbhtc3.seq - HTC (high throughput cDNA sequencing) entries, part 3.
460. gbhtc4.seq - HTC (high throughput cDNA sequencing) entries, part 4.
461. gbcon.seq - CON division entries (see description below for details)
462. gbchg.txt - Accession numbers of entries updated since the previous release.
463. gbdel.txt - Accession numbers of entries deleted since the previous release.
464. 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 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 134.0 flatfiles require roughly 96.94 GB (sequence
files only) or 109.9 GB (including the 'short directory' and 'index' 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
752778260 gbacc.idx
511319704 gbaut1.idx
502206726 gbaut10.idx
510248187 gbaut11.idx
501835240 gbaut12.idx
539669774 gbaut13.idx
500740540 gbaut14.idx
500200864 gbaut15.idx
500000039 gbaut16.idx
500796320 gbaut17.idx
503158225 gbaut18.idx
109750504 gbaut19.idx
501032975 gbaut2.idx
500547672 gbaut3.idx
509831367 gbaut4.idx
504871464 gbaut5.idx
513257418 gbaut6.idx
501968039 gbaut7.idx
504489136 gbaut8.idx
502431857 gbaut9.idx
250016378 gbbct1.seq
250544418 gbbct2.seq
250001019 gbbct3.seq
250044533 gbbct4.seq
250003289 gbbct5.seq
172441091 gbbct6.seq
963470 gbchg.txt
15835720 gbcon.seq
1295 gbdel.txt
230687980 gbest1.seq
230689155 gbest10.seq
230687721 gbest100.seq
230689819 gbest101.seq
230688449 gbest102.seq
230690349 gbest103.seq
230688558 gbest104.seq
230687889 gbest105.seq
230689745 gbest106.seq
230688633 gbest107.seq
230690076 gbest108.seq
230689840 gbest109.seq
230687882 gbest11.seq
230688485 gbest110.seq
230688454 gbest111.seq
230689471 gbest112.seq
230690089 gbest113.seq
230690256 gbest114.seq
230690843 gbest115.seq
230689893 gbest116.seq
230690897 gbest117.seq
230689334 gbest118.seq
230688844 gbest119.seq
230689763 gbest12.seq
230690064 gbest120.seq
230689939 gbest121.seq
230687728 gbest122.seq
230687876 gbest123.seq
230689795 gbest124.seq
230689991 gbest125.seq
230690019 gbest126.seq
230689886 gbest127.seq
230688141 gbest128.seq
230690114 gbest129.seq
230687861 gbest13.seq
230690316 gbest130.seq
230687813 gbest131.seq
230688072 gbest132.seq
230687831 gbest133.seq
230690599 gbest134.seq
230689121 gbest135.seq
230688954 gbest136.seq
230689572 gbest137.seq
230690193 gbest138.seq
230689459 gbest139.seq
230687494 gbest14.seq
230689104 gbest140.seq
230687639 gbest141.seq
230690212 gbest142.seq
230690497 gbest143.seq
230690190 gbest144.seq
230690128 gbest145.seq
230692458 gbest146.seq
230688249 gbest147.seq
230695599 gbest148.seq
230689488 gbest149.seq
230690031 gbest15.seq
230687752 gbest150.seq
230689038 gbest151.seq
230688956 gbest152.seq
230687519 gbest153.seq
230688469 gbest154.seq
230688567 gbest155.seq
230689842 gbest156.seq
230687967 gbest157.seq
230689917 gbest158.seq
230688865 gbest159.seq
230687497 gbest16.seq
230690698 gbest160.seq
230688660 gbest161.seq
230688383 gbest162.seq
230689185 gbest163.seq
230689153 gbest164.seq
230690271 gbest165.seq
230690390 gbest166.seq
230687497 gbest167.seq
230689892 gbest168.seq
230689826 gbest169.seq
230687810 gbest17.seq
230687923 gbest170.seq
230689160 gbest171.seq
230687610 gbest172.seq
230689915 gbest173.seq
230690148 gbest174.seq
230688997 gbest175.seq
230687679 gbest176.seq
230688656 gbest177.seq
230687848 gbest178.seq
230690115 gbest179.seq
230689465 gbest18.seq
230688417 gbest180.seq
230687574 gbest181.seq
230691269 gbest182.seq
230689517 gbest183.seq
230689147 gbest184.seq
230688849 gbest185.seq
230688949 gbest186.seq
230688181 gbest187.seq
230688457 gbest188.seq
230687555 gbest189.seq
230687586 gbest19.seq
164781018 gbest190.seq
163613105 gbest191.seq
170107774 gbest192.seq
171141431 gbest193.seq
171673663 gbest194.seq
168051469 gbest195.seq
166767927 gbest196.seq
166792690 gbest197.seq
168614758 gbest198.seq
168071701 gbest199.seq
230690391 gbest2.seq
230688400 gbest20.seq
167506849 gbest200.seq
174472980 gbest201.seq
164556570 gbest202.seq
173058019 gbest203.seq
164246785 gbest204.seq
166554093 gbest205.seq
171247032 gbest206.seq
172497208 gbest207.seq
169263846 gbest208.seq
167118136 gbest209.seq
230690082 gbest21.seq
167523261 gbest210.seq
168936991 gbest211.seq
168369810 gbest212.seq
167840298 gbest213.seq
167200902 gbest214.seq
179558169 gbest215.seq
182448467 gbest216.seq
176388678 gbest217.seq
206922937 gbest218.seq
230687849 gbest219.seq
230687787 gbest22.seq
230687901 gbest220.seq
230687816 gbest221.seq
230690273 gbest222.seq
230690682 gbest223.seq
230687881 gbest224.seq
230688567 gbest225.seq
230688843 gbest226.seq
230687513 gbest227.seq
230689255 gbest228.seq
230689136 gbest229.seq
230689003 gbest23.seq
230690346 gbest230.seq
230689039 gbest231.seq
230688608 gbest232.seq
230687879 gbest233.seq
230690182 gbest234.seq
230690601 gbest235.seq
230688451 gbest236.seq
230688943 gbest237.seq
230688185 gbest238.seq
230689196 gbest239.seq
230689742 gbest24.seq
63838045 gbest240.seq
230689744 gbest25.seq
230689223 gbest26.seq
230689439 gbest27.seq
230689937 gbest28.seq
230688421 gbest29.seq
230688556 gbest3.seq
230687475 gbest30.seq
230688436 gbest31.seq
230689587 gbest32.seq
230688990 gbest33.seq
230689257 gbest34.seq
230688862 gbest35.seq
211918835 gbest36.seq
210096283 gbest37.seq
210229122 gbest38.seq
218219361 gbest39.seq
230689876 gbest4.seq
216563192 gbest40.seq
216303129 gbest41.seq
217288708 gbest42.seq
230687774 gbest43.seq
230689557 gbest44.seq
222885965 gbest45.seq
230689600 gbest46.seq
230687926 gbest47.seq
230687556 gbest48.seq
230690151 gbest49.seq
165267638 gbest5.seq
230688419 gbest50.seq
230687804 gbest51.seq
230688898 gbest52.seq
230689765 gbest53.seq
230689305 gbest54.seq
230691429 gbest55.seq
230688469 gbest56.seq
230689628 gbest57.seq
230690059 gbest58.seq
230689012 gbest59.seq
180014575 gbest6.seq
230690076 gbest60.seq
230690646 gbest61.seq
209803127 gbest62.seq
209415333 gbest63.seq
208947707 gbest64.seq
209157310 gbest65.seq
210507566 gbest66.seq
209989846 gbest67.seq
208816674 gbest68.seq
209406174 gbest69.seq
230687546 gbest7.seq
210709936 gbest70.seq
206665409 gbest71.seq
206710780 gbest72.seq
208314262 gbest73.seq
208775985 gbest74.seq
215237400 gbest75.seq
230688893 gbest76.seq
230692583 gbest77.seq
230687964 gbest78.seq
227811960 gbest79.seq
230689635 gbest8.seq
217571732 gbest80.seq
218884614 gbest81.seq
230687862 gbest82.seq
230689025 gbest83.seq
230688697 gbest84.seq
230689314 gbest85.seq
230687442 gbest86.seq
230687590 gbest87.seq
230689547 gbest88.seq
230688182 gbest89.seq
230687830 gbest9.seq
230688079 gbest90.seq
230690471 gbest91.seq
230687806 gbest92.seq
230687550 gbest93.seq
230688625 gbest94.seq
230689637 gbest95.seq
230690255 gbest96.seq
230688988 gbest97.seq
230687907 gbest98.seq
230687908 gbest99.seq
28682388 gbgen.idx
209716254 gbgss1.seq
209717589 gbgss10.seq
209718595 gbgss11.seq
209719710 gbgss12.seq
209715944 gbgss13.seq
209717038 gbgss14.seq
209718117 gbgss15.seq
209716851 gbgss16.seq
209717045 gbgss17.seq
209717604 gbgss18.seq
209719433 gbgss19.seq
209717078 gbgss2.seq
209719917 gbgss20.seq
209716862 gbgss21.seq
209718463 gbgss22.seq
209718439 gbgss23.seq
209717920 gbgss24.seq
209717859 gbgss25.seq
209717202 gbgss26.seq
209716127 gbgss27.seq
209717394 gbgss28.seq
209716474 gbgss29.seq
209716137 gbgss3.seq
209719025 gbgss30.seq
209718092 gbgss31.seq
209716521 gbgss32.seq
209717432 gbgss33.seq
209719210 gbgss34.seq
209715925 gbgss35.seq
209716526 gbgss36.seq
209717810 gbgss37.seq
209717857 gbgss38.seq
209716182 gbgss39.seq
209717320 gbgss4.seq
209717521 gbgss40.seq
209716461 gbgss41.seq
209716670 gbgss42.seq
209716470 gbgss43.seq
209716240 gbgss44.seq
209716257 gbgss45.seq
209718718 gbgss46.seq
209718733 gbgss47.seq
209718931 gbgss48.seq
209716269 gbgss49.seq
209718666 gbgss5.seq
209717902 gbgss50.seq
209717454 gbgss51.seq
209718302 gbgss52.seq
209717500 gbgss53.seq
209716951 gbgss54.seq
26626545 gbgss55.seq
250002169 gbgss56.seq
250001674 gbgss57.seq
250000313 gbgss58.seq
250000916 gbgss59.seq
209717526 gbgss6.seq
250002584 gbgss60.seq
250000696 gbgss61.seq
250003210 gbgss62.seq
250003827 gbgss63.seq
250001562 gbgss64.seq
250000355 gbgss65.seq
28151696 gbgss66.seq
209718159 gbgss7.seq
209717588 gbgss8.seq
209717682 gbgss9.seq
250001113 gbhtc1.seq
250009741 gbhtc2.seq
250001826 gbhtc3.seq
62469810 gbhtc4.seq
250166277 gbhtg1.seq
250040218 gbhtg10.seq
250059638 gbhtg11.seq
250065699 gbhtg12.seq
250311384 gbhtg13.seq
250265867 gbhtg14.seq
250017983 gbhtg15.seq
250157096 gbhtg16.seq
250179996 gbhtg17.seq
250220124 gbhtg18.seq
250211360 gbhtg19.seq
250020817 gbhtg2.seq
250136167 gbhtg20.seq
250003080 gbhtg21.seq
250089285 gbhtg22.seq
250137084 gbhtg23.seq
250116184 gbhtg24.seq
250159644 gbhtg25.seq
250198659 gbhtg26.seq
250064034 gbhtg27.seq
250118742 gbhtg28.seq
250003306 gbhtg29.seq
250023801 gbhtg3.seq
250015429 gbhtg30.seq
250204810 gbhtg31.seq
250152084 gbhtg32.seq
250121490 gbhtg33.seq
250211359 gbhtg34.seq
250080977 gbhtg35.seq
250128302 gbhtg36.seq
250031737 gbhtg37.seq
250157633 gbhtg38.seq
250051952 gbhtg39.seq
250071851 gbhtg4.seq
250186700 gbhtg40.seq
250108856 gbhtg41.seq
250146703 gbhtg42.seq
250020209 gbhtg43.seq
250151566 gbhtg44.seq
250033624 gbhtg45.seq
250001237 gbhtg46.seq
250195881 gbhtg47.seq
250061916 gbhtg48.seq
250193247 gbhtg49.seq
250051812 gbhtg5.seq
250087020 gbhtg50.seq
250134935 gbhtg51.seq
250301662 gbhtg52.seq
250120329 gbhtg53.seq
250133960 gbhtg54.seq
250001087 gbhtg55.seq
250203578 gbhtg56.seq
250026792 gbhtg57.seq
105485966 gbhtg58.seq
250140012 gbhtg6.seq
250145316 gbhtg7.seq
250224008 gbhtg8.seq
250089154 gbhtg9.seq
250203058 gbinv1.seq
250258702 gbinv2.seq
250002585 gbinv3.seq
250001510 gbinv4.seq
236608334 gbinv5.seq
574068517 gbjou.idx
518672747 gbkey.idx
156293247 gbmam.seq
10934659 gbnew.txt
250000176 gbpat1.seq
250000357 gbpat2.seq
250003952 gbpat3.seq
250001434 gbpat4.seq
250001403 gbpat5.seq
250001068 gbpat6.seq
117579348 gbpat7.seq
19752438 gbphg.seq
250119611 gbpln1.seq
250001777 gbpln2.seq
250111708 gbpln3.seq
250000524 gbpln4.seq
250006521 gbpln5.seq
250004819 gbpln6.seq
105739472 gbpln7.seq
250158230 gbpri1.seq
250211773 gbpri10.seq
250021017 gbpri11.seq
250065672 gbpri12.seq
250131590 gbpri13.seq
250055442 gbpri14.seq
250108617 gbpri15.seq
250004454 gbpri16.seq
250198702 gbpri17.seq
250091522 gbpri18.seq
250008945 gbpri19.seq
250272932 gbpri2.seq
250006628 gbpri20.seq
250077504 gbpri21.seq
250001677 gbpri22.seq
250003623 gbpri23.seq
216554044 gbpri24.seq
250073925 gbpri3.seq
250040487 gbpri4.seq
250097062 gbpri5.seq
250206824 gbpri6.seq
250147743 gbpri7.seq
250253208 gbpri8.seq
250127455 gbpri9.seq
147019 gbrel.txt
250232095 gbrod1.seq
250282691 gbrod2.seq
250010883 gbrod3.seq
250138500 gbrod4.seq
250000599 gbrod5.seq
212706412 gbrod6.seq
1842894815 gbsdr.txt
1464542 gbsec.idx
250002792 gbsts1.seq
178489112 gbsts2.seq
34957380 gbsyn.seq
1415158 gbuna.seq
250001150 gbvrl1.seq
250000242 gbvrl2.seq
99169886 gbvrl3.seq
250000457 gbvrt1.seq
167073400 gbvrt2.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 sequence
data file:
Division Entries Bases
BCT1 21596 102382590
BCT2 7637 107498513
BCT3 62327 89871050
BCT4 11766 108452239
BCT5 45195 92850148
BCT6 28088 63145689
EST1 68333 26365039
EST10 76745 29941526
EST100 72091 33383881
EST101 70046 29552935
EST102 66749 37956190
EST103 69054 36788216
EST104 68321 43630907
EST105 73315 33973380
EST106 75525 34886994
EST107 74805 27322217
EST108 73926 35813057
EST109 74256 35289236
EST11 75365 28764290
EST110 69091 42159211
EST111 80755 44425121
EST112 77294 45980900
EST113 69518 44319636
EST114 67239 42405939
EST115 74641 50169030
EST116 69941 42589101
EST117 75925 44389642
EST118 73376 46257369
EST119 71976 47752614
EST12 77514 30859409
EST120 73715 50885304
EST121 79158 40284160
EST122 76141 30926872
EST123 79104 39779856
EST124 77834 43170893
EST125 76990 47231058
EST126 61053 28213275
EST127 75012 41644508
EST128 68132 37651074
EST129 67978 38441910
EST13 77206 29188394
EST130 71206 42693674
EST131 73716 47895854
EST132 66695 38302641
EST133 73504 41889065
EST134 68879 39984693
EST135 61359 37999883
EST136 87052 47272289
EST137 93662 52993914
EST138 72211 38139587
EST139 72896 38526533
EST14 78694 31971652
EST140 94790 50686280
EST141 104189 56553052
EST142 94295 54243712
EST143 69942 40515459
EST144 66450 32342609
EST145 62677 29468947
EST146 57857 30279713
EST147 62896 31166732
EST148 54315 27366151
EST149 79905 53557138
EST15 73849 31229292
EST150 69056 37446461
EST151 72567 52843161
EST152 72021 40944718
EST153 61117 30604490
EST154 64718 39698762
EST155 68125 31299642
EST156 63958 46388103
EST157 67714 39062050
EST158 72456 40775101
EST159 68487 43325892
EST16 75558 33227263
EST160 63893 36771203
EST161 64843 42431665
EST162 68202 30922910
EST163 76230 31533585
EST164 70984 44722079
EST165 79310 39589408
EST166 63374 32891005
EST167 69682 49738763
EST168 69780 46803835
EST169 68110 36039891
EST17 83275 34240426
EST170 69516 44810075
EST171 69297 53342332
EST172 69804 35627348
EST173 70350 42572831
EST174 70724 61206192
EST175 64790 47188787
EST176 63898 46695358
EST177 63492 47023620
EST178 65512 45433821
EST179 66212 49918442
EST18 80511 32258104
EST180 62652 42390975
EST181 65878 39763283
EST182 60172 33661393
EST183 70167 36048163
EST184 85333 55661323
EST185 70103 42964356
EST186 99830 62077654
EST187 106706 65773194
EST188 108425 63552711
EST189 69279 39506530
EST19 78864 32347888
EST190 27688 10426656
EST191 27783 10421097
EST192 26692 9794392
EST193 26516 9509862
EST194 26472 9058418
EST195 26920 9917349
EST196 27068 9643815
EST197 26974 9801870
EST198 26671 10906971
EST199 26673 11549987
EST2 75036 28805559
EST20 74340 30151689
EST200 26807 10792216
EST201 25790 9213063
EST202 27547 9139114
EST203 26198 9475977
EST204 27637 11102666
EST205 27303 10851705
EST206 26486 11162627
EST207 25981 11725501
EST208 26608 11012523
EST209 26961 10839441
EST21 73739 34280583
EST210 26795 11612294
EST211 26675 11333740
EST212 26710 10750091
EST213 26778 10654718
EST214 26988 10411701
EST215 24864 9929026
EST216 24292 17026213
EST217 25261 16816001
EST218 66997 27771375
EST219 88744 40110585
EST22 75845 30425552
EST220 71628 42281502
EST221 77480 44957830
EST222 64694 48034759
EST223 64981 34165960
EST224 76344 38854440
EST225 101483 46623660
EST226 75181 42852392
EST227 63797 32783663
EST228 69522 33559149
EST229 69398 45390115
EST23 77247 32327528
EST230 74013 34232012
EST231 70547 37559160
EST232 92282 46780543
EST233 81455 26846102
EST234 71787 25592065
EST235 73647 27272289
EST236 72862 26519614
EST237 79946 27011984
EST238 73020 27196776
EST239 68402 29214016
EST24 75422 33725400
EST240 25466 8016006
EST25 72329 30722559
EST26 76170 31657442
EST27 76250 33173322
EST28 103680 49681700
EST29 70673 45967463
EST3 73894 29981502
EST30 82233 56312778
EST31 91496 50535789
EST32 97347 50088408
EST33 93534 43876718
EST34 94430 48994090
EST35 100729 45229106
EST36 60920 18153612
EST37 59611 15726287
EST38 59301 15883678
EST39 61114 18734645
EST4 74402 28251763
EST40 43551 11917409
EST41 43169 11871537
EST42 43063 11394655
EST43 82290 34167381
EST44 95405 43437722
EST45 90300 46964577
EST46 84816 39937416
EST47 106902 56271519
EST48 94185 45730195
EST49 76130 32718551
EST5 48500 15380287
EST50 68317 29978139
EST51 71648 31147562
EST52 71565 30118836
EST53 83444 33525785
EST54 74057 29370327
EST55 65720 28099618
EST56 70407 31151888
EST57 76839 36591042
EST58 73322 32098325
EST59 75267 27424427
EST6 55669 17851521
EST60 79405 30098220
EST61 74839 33439059
EST62 40227 11416519
EST63 40191 11258966
EST64 40319 12688158
EST65 40626 12283415
EST66 40604 12464144
EST67 40505 12929203
EST68 40520 12563868
EST69 40367 12126458
EST7 74567 29348606
EST70 40331 12317611
EST71 41163 12341935
EST72 41325 12273556
EST73 41216 13124332
EST74 41022 13053286
EST75 43542 12505456
EST76 43634 19772789
EST77 40480 24759217
EST78 42787 18619549
EST79 44493 18386759
EST8 76202 30681145
EST80 49531 21425585
EST81 48971 21001837
EST82 69260 31626982
EST83 72405 27420367
EST84 74792 29457197
EST85 75198 41099137
EST86 78248 41014424
EST87 77082 44137921
EST88 76818 35286142
EST89 74838 43327515
EST9 77738 29969805
EST90 71785 36653552
EST91 74132 37694314
EST92 73459 39466397
EST93 75062 41180069
EST94 70521 40619301
EST95 69163 36296812
EST96 73439 36228415
EST97 72925 46685730
EST98 72602 44775379
EST99 71109 42399662
GSS1 83277 35678570
GSS10 66627 34169864
GSS11 68874 40613310
GSS12 62893 31916167
GSS13 65571 34558357
GSS14 69182 36063181
GSS15 65564 29704457
GSS16 64460 29761099
GSS17 71537 41723025
GSS18 65569 33908077
GSS19 60267 27422241
GSS2 83479 35629718
GSS20 52122 27247000
GSS21 52559 26105819
GSS22 53719 23106465
GSS23 57863 33348274
GSS24 58834 30408244
GSS25 52941 25074060
GSS26 60530 39572406
GSS27 64379 27386881
GSS28 54061 22151504
GSS29 55469 27563344
GSS3 81440 38312461
GSS30 66678 31551318
GSS31 55432 31939649
GSS32 85551 38109588
GSS33 69653 36857703
GSS34 67999 38917765
GSS35 64905 41679289
GSS36 73292 35912844
GSS37 70018 37054191
GSS38 71518 37988347
GSS39 85904 56293897
GSS4 74354 38120527
GSS40 85999 57119377
GSS41 80919 41988671
GSS42 84543 50795470
GSS43 79147 35163980
GSS44 76355 28872698
GSS45 74344 48261969
GSS46 74153 52331049
GSS47 69190 48236998
GSS48 66240 43918343
GSS49 66370 43660144
GSS5 71183 38065917
GSS50 72632 40119666
GSS51 72987 37282206
GSS52 82155 58968866
GSS53 79057 65449459
GSS54 81128 42064522
GSS55 11467 6637717
GSS56 88066 66600405
GSS57 84358 63376716
GSS58 95585 37385508
GSS59 107660 68662815
GSS6 70635 35406886
GSS60 89142 67468980
GSS61 72987 60702708
GSS62 69797 58861587
GSS63 67185 63891159
GSS64 73290 54303215
GSS65 109275 52299560
GSS66 10980 4826244
GSS7 70944 35613122
GSS8 71353 36474681
GSS9 68975 34298875
HTC1 27633 44429991
HTC2 25937 58768399
HTC3 68998 74245658
HTC4 27793 19656473
HTG1 1329 190717330
HTG10 1200 189698968
HTG11 1507 186574501
HTG12 1003 192124798
HTG13 720 192731548
HTG14 740 192717246
HTG15 724 192428665
HTG16 799 192527990
HTG17 738 192651498
HTG18 770 192705317
HTG19 2119 178479622
HTG2 2239 188311891
HTG20 1153 188158512
HTG21 1097 189410175
HTG22 1018 190184475
HTG23 755 192449665
HTG24 943 190776185
HTG25 950 190872047
HTG26 926 191128210
HTG27 839 191546058
HTG28 774 192395396
HTG29 959 190721219
HTG3 2620 187786744
HTG30 874 191414878
HTG31 972 190868393
HTG32 1077 189405112
HTG33 1028 190051061
HTG34 1000 190698444
HTG35 1064 189718916
HTG36 968 190707407
HTG37 929 192293110
HTG38 1077 190346287
HTG39 980 191512320
HTG4 2704 189971284
HTG40 913 191865370
HTG41 872 192399574
HTG42 839 192028035
HTG43 901 191667960
HTG44 977 191092458
HTG45 968 191402643
HTG46 932 192037142
HTG47 1049 190713435
HTG48 1084 190580657
HTG49 1213 189643456
HTG5 1292 188380727
HTG50 1125 190370249
HTG51 1523 188441264
HTG52 1263 190360112
HTG53 1047 193686190
HTG54 1028 194141110
HTG55 1300 191028344
HTG56 1218 194453010
HTG57 1145 193497698
HTG58 467 77559044
HTG6 1295 187780865
HTG7 1249 188336389
HTG8 1258 188261569
HTG9 1234 189002604
INV1 9113 174900882
INV2 1886 165889064
INV3 63142 87722789
INV4 45533 99519883
INV5 36919 103826683
MAM 46170 53195994
PAT1 222820 70209374
PAT2 165449 90181131
PAT3 146501 88567863
PAT4 115891 113659130
PAT5 133175 63219683
PAT6 104113 63511092
PAT7 94177 28685881
PHG 2285 7507502
PLN1 19523 140326561
PLN2 69366 91012321
PLN3 49338 108579623
PLN4 29546 122097380
PLN5 58596 73270629
PLN6 47807 108998458
PLN7 17751 43296091
PRI1 13782 155383696
PRI10 1355 173256797
PRI11 1282 175137046
PRI12 1533 176880153
PRI13 1675 177512103
PRI14 36676 129564937
PRI15 30205 128655916
PRI16 1597 178943536
PRI17 1687 181243420
PRI18 2043 183956468
PRI19 1824 186951052
PRI2 1426 173925402
PRI20 26010 136319482
PRI21 17642 159689390
PRI22 30530 135979695
PRI23 36936 127431012
PRI24 52467 83806655
PRI3 1257 182406861
PRI4 1272 177319431
PRI5 1141 173960155
PRI6 1232 180452855
PRI7 1194 175682057
PRI8 1316 168306679
PRI9 1258 178258634
ROD1 6817 179730503
ROD2 14770 171567007
ROD3 9732 179505778
ROD4 1195 194116640
ROD5 13779 168310418
ROD6 51202 76540923
STS1 90167 35759094
STS2 68025 31306797
SYN 7886 14140118
UNA 616 329869
VRL1 73945 63915414
VRL2 77206 62782524
VRL3 25888 31224257
VRT1 57593 100563517
VRT2 39479 66856880
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 134.0 (chloroplast and mitochon-
drial sequences not included):
Entries Bases Species
6505879 9571083260 Homo sapiens
4809688 5485813183 Mus musculus
659541 5402127949 Rattus norvegicus
346582 692395973 Drosophila melanogaster
464804 618698048 Danio rerio
170783 584093798 Oryza sativa (japonica cultivar-group)
567860 386351030 Brassica oleracea
466368 380958842 Arabidopsis thaliana
404230 301845630 Gallus gallus
499186 294088818 Ciona intestinalis
516762 262846445 Zea mays
199202 221942726 Caenorhabditis elegans
418033 207360111 Triticum aestivum
161076 171073629 Pan troglodytes
189153 170383328 Tetraodon nigroviridis
263124 157037944 Xenopus laevis
282042 156157876 Hordeum vulgare subsp. vulgare
320222 149834937 Glycine max
262206 148265441 Bos taurus
227300 145710747 Anopheles gambiae
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
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 index files and the lists of new, changed, and
deleted records, each of the 464 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, '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 April 2003
NCBI-GenBank Flat File Release 134.0
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) presented 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.
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/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/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 134.0) 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,
Michael Fetchko, Anjanette Johnston, Pierre Ledoux, Richard McVeigh,
Leonie Misquitta, Ilene Mizrachi, DeAnne Olsen Cravaritis,
Chris O'Sullivan, David Rasko, Leigh Riley, Gert Roosen, Susan
Schafer, Suh-suh Wang, Jane Weisemann, Steven Wilhite, and
Linda Yankie
Data Management and Preparation
Vladimir Alekseyev, Serge Bazhin, Anton Butanaev, Mark Cavanaugh,
Hsiu-Chuan Chen, Jonathan Kans, Michael Kimelman, Jim Ostell,
Joel Plotkin, Karl Sirotkin, Vladimir Soussov, Elena Starchenko,
Hanzhen Sun, Tatiana Tatusov, Carolyn Tolstoshev, Jane Weisemann,
Eugene Yaschenko
Database Administration
Helen Epting, Slava Khotomliansky, 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
