Release Notes For GenBank Release 133
GBREL.TXT Genetic Sequence Data Bank
December 15 2002
NCBI-GenBank Flat File Release 133.0
Distribution Release Notes
22318883 loci, 28507990166 bases, from 22318883 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 133.0
1.2 Cutoff Date
1.3 Important Changes in Release 133.0
1.4 Upcoming Changes
1.5 Request for Direct Submission of Sequence Data
1.6 Organization of This Document
2. ORGANIZATION OF DATA FILES
2.1 Overview
2.2 Files
2.2.1 File Descriptions
2.2.5 File Sizes
2.2.6 Per-Division Statistics
2.2.7 Selected Per-Organism Statistics
2.2.8 Growth of GenBank
3. FILE FORMATS
3.1 File Header Information
3.2 Directory Files
3.2.1 Short Directory File
3.3 Index Files
3.3.1 Accession Number Index File
3.3.2 Keyword Phrase Index File
3.3.3 Author Name Index File
3.3.4 Journal Citation Index File
3.3.5 Gene Name Index
3.4 Sequence Entry Files
3.4.1 File Organization
3.4.2 Entry Organization
3.4.3 Sample Sequence Data File
3.4.4 LOCUS Format
3.4.5 DEFINITION Format
3.4.5.1 DEFINITION Format for NLM Entries
3.4.6 ACCESSION Format
3.4.7 VERSION Format
3.4.8 KEYWORDS Format
3.4.9 SEGMENT Format
3.4.10 SOURCE Format
3.4.11 REFERENCE Format
3.4.12 FEATURES Format
3.4.12.1 Feature Key Names
3.4.12.2 Feature Location
3.4.12.3 Feature Qualifiers
3.4.12.4 Cross-Reference Information
3.4.12.5 Feature Table Examples
3.4.13 ORIGIN Format
3.4.14 SEQUENCE Format
4. ALTERNATE RELEASES
5. KNOWN PROBLEMS OF THE GENBANK DATABASE
5.1 Incorrect Gene Symbols in Entries and Index
6. GENBANK ADMINISTRATION
6.1 Registered Trademark Notice
6.2 Citing GenBank
6.3 GenBank Distribution Formats and Media
6.4 Other Methods of Accessing GenBank Data
6.5 Request for Corrections and Comments
6.6 Credits and Acknowledgments
6.7 Disclaimer
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1. INTRODUCTION
1.1 Release 133.0
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 133.0 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, 133.0, incorporates data available to the collaborating
databases as of December 31, 2002. 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 133.0
1.3.1 Organizational changes
The total number of sequence data files increased by 55 with this release:
- the EST division is now comprised of 235 files
- the GSS division is now comprised of 63 files
- the HTC division is now comprised of 3 files
- the HTG division is now comprised of 57 files
- the PAT division is now comprised of 7 files
- the PLN division is now comprised of 7 files
- the PRI division is now comprised of 24 files
- the ROD division is now comprised of 6 files
However, note that there was a special supplemental file (gbsup.seq) for
full-length-insert cDNA sequences in Release 132.0.
The fli-cDNA sequences *should* have been present in the standard
divisional files. The problem that required the use of the supplemental
file has been corrected, so this release does not include gbsup.seq .
If the removal of gbsup.seq is taken into account, the total number of
sequence data files increased by 54 .
1.3.2 New SET Data File For The ASN.1 Representation
Some phylogenetic and mutational studies involve sequences from more
than one of the 'taxonomic' divisions of GenBank. For example, a phylogenetic
study might involve sequences obtained from human (PRI) and non-primate
mammalian (MAM) sources.
Such studies, often with associated sequence alignments, are maintained
and edited as a single unit in the underlying data representation (ASN.1)
utilized by the NCBI.
When generating GenBank flatfiles from such studies, the component
sequences are processed in such a way that they are individually directed
to an appropriate divisional file. For example, the human sequences to a
PRI division file, the other mammalian sequences to the MAM division file.
In the past, we have mimicked this behavior for the ASN.1 version of
GenBank releases by splitting the studies into their components, and
splicing them into an appropriate divisional ASN.1 file (eg, gbpri1.aso
and gbmam.aso) .
This practice has clear disadvantages: the components of the studies
really should *not* be separated; and the post-processing of these special
studies adds considerable overhead to release processing.
Starting with this December 2002 release, we have ceased this practice
and have introduced a new ASN.1 data file for such multi-divisional
studies at ftp://ftp.ncbi.nih.gov/ncbi-asn1 . The new file is :
gbset.aso
1.3.3 Reduction In The Number Of ASN.1 Data Files
The sizes of many of the files for the ASN.1 version of GenBank releases
(see ftp://ftp.ncbi.nih.gov/ncbi-asn1 ) used to be well below the 250 MB utilized
for the GenBank flatfile version. For example, the PRI division ASN.1 files
were about 140 MB apiece, and the HTG division files are about 190 MB apiece,
for GenBank Release 132.0 .
This was due to the fact that the ASN.1 representation was originally
used to create the flatfile version, on a file-by-file basis, during release
generation. Since the ASN.1 version is more compact than the flatfile version,
the ASN.1 file sizes had to be less than 250 MB to yield 250 MB flatfiles.
Now that the ASN.1 and flatfile versions are created independently, the
sizes of the ASN.1 files can be increased without consequences for the
flatfiles.
Starting with this December 2002 release, the file size limit for all
ASN.1 files has been increased to 250MB, and as a result, the total number of
ASN.1 files has been significantly reduced.
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 133.0. Consider the gbgss55.seq file:
GBGSS1.SEQ Genetic Sequence Data Bank
December 15 2002
NCBI-GenBank Flat File Release 133.0
GSS Sequences (Part 1)
88062 loci, 66597557 bases, from 88062 reported sequences
Here, the filename and part number in the header is "1", though the file
has been renamed as "55" 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 * * Cumulative GenBank Update Products To Be Discontinued * *
As of GenBank Release 134.0 in February of 2002, the cumulative
GenBank Update (GBCU) products will be 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 is not uncommon
for GBCU products to approach 20% of the total database size. The flatfile
version, for example, has reached sizes in excess of 17 GB in recent weeks.
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, which will soon approach 20GB in size, we have decided
that the GBCU should be discontinued. We will analyze FTP logs and
proactively contact the larger centers which utilize the GBCU, to suggest
alternate processing strategies.
If large numbers of users are unable to switch to processing incremental
updates by February 2002, there is a possibility that the date for
discontinuing the GBCU might be pushed back to April.
We will keep users informed of the timetable for this important change
via these release notes and the GenBank newsgroup. And of course, we
welcome discussions of this change via the newsgroup.
1.4.2 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.
1.4.3 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"
1.4.4 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 a 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;
1.4.5 Third-Party Annotation and Consensus Sequences (TPA)
Pursuant to agreements made at the 2002 Collaborative Meeting, DDBJ/EMBL/GenBank
have undertaken the collection of a new class of sequence data : Third-Party
Annotation and Consensus Sequences (TPA).
The TPA data-collection will complement 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 as 'owner' of these 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 entries 'owned' by other groups, or
b) consist of a mixture of new & previously-existing sequences
TPA categories and requirements
-------------------------------
Users can submit re-annotations/re-assemblies of sequences already
present in DDBJ/EMBL/GenBank and owned by other groups to be
included in the Third Party Annotation (TPA) data-collection.
Categories of data submissions accepted for TPA include:
1. re-annotation/analysis of sequence(s) from DDBJ/EMBL/GenBank
2. mixtures of primary/non-primary sequences, including regions of
new and existing sequence (e.g. filling gaps in a sequence
with data from HTG or EST projects, or newly sequenced data)
3. TPA sequences based on NCBI/Ensembl trace archive data
4. TPA sequences based on Whole Genome Shotgun (WGS) sequences
Consensus sequences from multiple organisms are not accepted.
The TPA dataset is primarily intended as a means to present sequence
and annotation in support of actual biological discoveries, published
in the scientific literature, without requiring that every basepair
has actually been sequenced by the authors/submittors.
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.
Third Party Annotation (TPA) records include a mandatory 'TPA-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 TPA-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
Preliminary exchange of TPA records among DDBJ/EMBL/GenBank are
underway. Within two months, data products will be made available at
the GenBank FTP site for TPA sequences. Details about those products,
sample records, and instructions for submission of TPA data, will
be communicated via the GenBank newsgroup:
http://net.bio.net/hypermail/genbankb/
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 449 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. gbjou.idx - Index of the entries according to journal citation.
24. gbgen.idx - Index of the entries according to gene names.
25. gbsec.idx - Index of the entries according to secondary accession number.
26. gbpri1.seq - Primate sequence entries, part 1.
27. gbpri2.seq - Primate sequence entries, part 2.
28. gbpri3.seq - Primate sequence entries, part 3.
29. gbpri4.seq - Primate sequence entries, part 4.
30. gbpri5.seq - Primate sequence entries, part 5.
31. gbpri6.seq - Primate sequence entries, part 6.
32. gbpri7.seq - Primate sequence entries, part 7.
33. gbpri8.seq - Primate sequence entries, part 8.
34. gbpri9.seq - Primate sequence entries, part 9.
35. gbpri10.seq - Primate sequence entries, part 10.
36. gbpri11.seq - Primate sequence entries, part 11.
37. gbpri12.seq - Primate sequence entries, part 12.
38. gbpri13.seq - Primate sequence entries, part 13.
39. gbpri14.seq - Primate sequence entries, part 14.
40. gbpri15.seq - Primate sequence entries, part 15.
41. gbpri16.seq - Primate sequence entries, part 16.
42. gbpri17.seq - Primate sequence entries, part 17.
43. gbpri18.seq - Primate sequence entries, part 18.
44. gbpri19.seq - Primate sequence entries, part 19.
45. gbpri20.seq - Primate sequence entries, part 20.
46. gbpri21.seq - Primate sequence entries, part 21.
47. gbpri22.seq - Primate sequence entries, part 22.
48. gbpri23.seq - Primate sequence entries, part 23.
49. gbpri24.seq - Primate sequence entries, part 24.
50. gbrod1.seq - Rodent sequence entries, part 1.
51. gbrod2.seq - Rodent sequence entries, part 2.
52. gbrod3.seq - Rodent sequence entries, part 3.
53. gbrod4.seq - Rodent sequence entries, part 4.
54. gbrod5.seq - Rodent sequence entries, part 5.
55. gbrod6.seq - Rodent sequence entries, part 6.
56. gbmam.seq - Other mammalian sequence entries.
57. gbvrt1.seq - Other vertebrate sequence entries, part 1.
58. gbvrt2.seq - Other vertebrate sequence entries, part 2.
59. gbinv1.seq - Invertebrate sequence entries, part 1.
60. gbinv2.seq - Invertebrate sequence entries, part 2.
61. gbinv3.seq - Invertebrate sequence entries, part 3.
62. gbinv4.seq - Invertebrate sequence entries, part 4.
63. gbinv5.seq - Invertebrate sequence entries, part 5.
64. gbpln1.seq - Plant sequence entries (including fungi and algae), part 1.
65. gbpln2.seq - Plant sequence entries (including fungi and algae), part 2.
66. gbpln3.seq - Plant sequence entries (including fungi and algae), part 3.
67. gbpln4.seq - Plant sequence entries (including fungi and algae), part 4.
68. gbpln5.seq - Plant sequence entries (including fungi and algae), part 5.
69. gbpln6.seq - Plant sequence entries (including fungi and algae), part 6.
70. gbpln7.seq - Plant sequence entries (including fungi and algae), part 7.
71. gbbct1.seq - Bacterial sequence entries, part 1.
72. gbbct2.seq - Bacterial sequence entries, part 2.
73. gbbct3.seq - Bacterial sequence entries, part 3.
74. gbbct4.seq - Bacterial sequence entries, part 4.
75. gbbct5.seq - Bacterial sequence entries, part 5.
76. gbbct6.seq - Bacterial sequence entries, part 6.
77. gbvrl1.seq - Viral sequence entries, part 1.
78. gbvrl2.seq - Viral sequence entries, part 2.
79. gbvrl3.seq - Viral sequence entries, part 3.
80. gbphg.seq - Phage sequence entries.
81. gbsyn.seq - Synthetic and chimeric sequence entries.
82. gbuna.seq - Unannotated sequence entries.
83. gbest1.seq - EST (expressed sequence tag) sequence entries, part 1.
84. gbest2.seq - EST (expressed sequence tag) sequence entries, part 2.
85. gbest3.seq - EST (expressed sequence tag) sequence entries, part 3.
86. gbest4.seq - EST (expressed sequence tag) sequence entries, part 4.
87. gbest5.seq - EST (expressed sequence tag) sequence entries, part 5.
88. gbest6.seq - EST (expressed sequence tag) sequence entries, part 6.
89. gbest7.seq - EST (expressed sequence tag) sequence entries, part 7.
90. gbest8.seq - EST (expressed sequence tag) sequence entries, part 8.
91. gbest9.seq - EST (expressed sequence tag) sequence entries, part 9.
92. gbest10.seq - EST (expressed sequence tag) sequence entries, part 10.
93. gbest11.seq - EST (expressed sequence tag) sequence entries, part 11.
94. gbest12.seq - EST (expressed sequence tag) sequence entries, part 12.
95. gbest13.seq - EST (expressed sequence tag) sequence entries, part 13.
96. gbest14.seq - EST (expressed sequence tag) sequence entries, part 14.
97. gbest15.seq - EST (expressed sequence tag) sequence entries, part 15.
98. gbest16.seq - EST (expressed sequence tag) sequence entries, part 16.
99. gbest17.seq - EST (expressed sequence tag) sequence entries, part 17.
100. gbest18.seq - EST (expressed sequence tag) sequence entries, part 18.
101. gbest19.seq - EST (expressed sequence tag) sequence entries, part 19.
102. gbest20.seq - EST (expressed sequence tag) sequence entries, part 20.
103. gbest21.seq - EST (expressed sequence tag) sequence entries, part 21.
104. gbest22.seq - EST (expressed sequence tag) sequence entries, part 22.
105. gbest23.seq - EST (expressed sequence tag) sequence entries, part 23.
106. gbest24.seq - EST (expressed sequence tag) sequence entries, part 24.
107. gbest25.seq - EST (expressed sequence tag) sequence entries, part 25.
108. gbest26.seq - EST (expressed sequence tag) sequence entries, part 26.
109. gbest27.seq - EST (expressed sequence tag) sequence entries, part 27.
110. gbest28.seq - EST (expressed sequence tag) sequence entries, part 28.
111. gbest29.seq - EST (expressed sequence tag) sequence entries, part 29.
112. gbest30.seq - EST (expressed sequence tag) sequence entries, part 30.
113. gbest31.seq - EST (expressed sequence tag) sequence entries, part 31.
114. gbest32.seq - EST (expressed sequence tag) sequence entries, part 32.
115. gbest33.seq - EST (expressed sequence tag) sequence entries, part 33.
116. gbest34.seq - EST (expressed sequence tag) sequence entries, part 34.
117. gbest35.seq - EST (expressed sequence tag) sequence entries, part 35.
118. gbest36.seq - EST (expressed sequence tag) sequence entries, part 36.
119. gbest37.seq - EST (expressed sequence tag) sequence entries, part 37.
120. gbest38.seq - EST (expressed sequence tag) sequence entries, part 38.
121. gbest39.seq - EST (expressed sequence tag) sequence entries, part 39.
122. gbest40.seq - EST (expressed sequence tag) sequence entries, part 40.
123. gbest41.seq - EST (expressed sequence tag) sequence entries, part 41.
124. gbest42.seq - EST (expressed sequence tag) sequence entries, part 42.
125. gbest43.seq - EST (expressed sequence tag) sequence entries, part 43.
126. gbest44.seq - EST (expressed sequence tag) sequence entries, part 44.
127. gbest45.seq - EST (expressed sequence tag) sequence entries, part 45.
128. gbest46.seq - EST (expressed sequence tag) sequence entries, part 46.
129. gbest47.seq - EST (expressed sequence tag) sequence entries, part 47.
130. gbest48.seq - EST (expressed sequence tag) sequence entries, part 48.
131. gbest49.seq - EST (expressed sequence tag) sequence entries, part 49.
132. gbest50.seq - EST (expressed sequence tag) sequence entries, part 50.
133. gbest51.seq - EST (expressed sequence tag) sequence entries, part 51.
134. gbest52.seq - EST (expressed sequence tag) sequence entries, part 52.
135. gbest53.seq - EST (expressed sequence tag) sequence entries, part 53.
136. gbest54.seq - EST (expressed sequence tag) sequence entries, part 54.
137. gbest55.seq - EST (expressed sequence tag) sequence entries, part 55.
138. gbest56.seq - EST (expressed sequence tag) sequence entries, part 56.
139. gbest57.seq - EST (expressed sequence tag) sequence entries, part 57.
140. gbest58.seq - EST (expressed sequence tag) sequence entries, part 58.
141. gbest59.seq - EST (expressed sequence tag) sequence entries, part 59.
142. gbest60.seq - EST (expressed sequence tag) sequence entries, part 60.
143. gbest61.seq - EST (expressed sequence tag) sequence entries, part 61.
144. gbest62.seq - EST (expressed sequence tag) sequence entries, part 62.
145. gbest63.seq - EST (expressed sequence tag) sequence entries, part 63.
146. gbest64.seq - EST (expressed sequence tag) sequence entries, part 64.
147. gbest65.seq - EST (expressed sequence tag) sequence entries, part 65.
148. gbest66.seq - EST (expressed sequence tag) sequence entries, part 66.
149. gbest67.seq - EST (expressed sequence tag) sequence entries, part 67.
150. gbest68.seq - EST (expressed sequence tag) sequence entries, part 68.
151. gbest69.seq - EST (expressed sequence tag) sequence entries, part 69.
152. gbest70.seq - EST (expressed sequence tag) sequence entries, part 70.
153. gbest71.seq - EST (expressed sequence tag) sequence entries, part 71.
154. gbest72.seq - EST (expressed sequence tag) sequence entries, part 72.
155. gbest73.seq - EST (expressed sequence tag) sequence entries, part 73.
156. gbest74.seq - EST (expressed sequence tag) sequence entries, part 74.
157. gbest75.seq - EST (expressed sequence tag) sequence entries, part 75.
158. gbest76.seq - EST (expressed sequence tag) sequence entries, part 76.
159. gbest77.seq - EST (expressed sequence tag) sequence entries, part 77.
160. gbest78.seq - EST (expressed sequence tag) sequence entries, part 78.
161. gbest79.seq - EST (expressed sequence tag) sequence entries, part 79.
162. gbest80.seq - EST (expressed sequence tag) sequence entries, part 80.
163. gbest81.seq - EST (expressed sequence tag) sequence entries, part 81.
164. gbest82.seq - EST (expressed sequence tag) sequence entries, part 82.
165. gbest83.seq - EST (expressed sequence tag) sequence entries, part 83.
166. gbest84.seq - EST (expressed sequence tag) sequence entries, part 84.
167. gbest85.seq - EST (expressed sequence tag) sequence entries, part 85.
168. gbest86.seq - EST (expressed sequence tag) sequence entries, part 86.
169. gbest87.seq - EST (expressed sequence tag) sequence entries, part 87.
170. gbest88.seq - EST (expressed sequence tag) sequence entries, part 88.
171. gbest89.seq - EST (expressed sequence tag) sequence entries, part 89
172. gbest90.seq - EST (expressed sequence tag) sequence entries, part 90.
173. gbest91.seq - EST (expressed sequence tag) sequence entries, part 91.
174. gbest92.seq - EST (expressed sequence tag) sequence entries, part 92.
175. gbest93.seq - EST (expressed sequence tag) sequence entries, part 93.
176. gbest94.seq - EST (expressed sequence tag) sequence entries, part 94.
177. gbest95.seq - EST (expressed sequence tag) sequence entries, part 95.
178. gbest96.seq - EST (expressed sequence tag) sequence entries, part 96.
179. gbest97.seq - EST (expressed sequence tag) sequence entries, part 97.
180. gbest98.seq - EST (expressed sequence tag) sequence entries, part 98.
181. gbest99.seq - EST (expressed sequence tag) sequence entries, part 99.
182. gbest100.seq - EST (expressed sequence tag) sequence entries, part 100.
183. gbest101.seq - EST (expressed sequence tag) sequence entries, part 101.
184. gbest102.seq - EST (expressed sequence tag) sequence entries, part 102.
185. gbest103.seq - EST (expressed sequence tag) sequence entries, part 103.
186. gbest104.seq - EST (expressed sequence tag) sequence entries, part 104.
187. gbest105.seq - EST (expressed sequence tag) sequence entries, part 105.
188. gbest106.seq - EST (expressed sequence tag) sequence entries, part 106.
189. gbest107.seq - EST (expressed sequence tag) sequence entries, part 107.
190. gbest108.seq - EST (expressed sequence tag) sequence entries, part 108.
191. gbest109.seq - EST (expressed sequence tag) sequence entries, part 109.
192. gbest110.seq - EST (expressed sequence tag) sequence entries, part 110.
193. gbest111.seq - EST (expressed sequence tag) sequence entries, part 111.
194. gbest112.seq - EST (expressed sequence tag) sequence entries, part 112.
195. gbest113.seq - EST (expressed sequence tag) sequence entries, part 113.
196. gbest114.seq - EST (expressed sequence tag) sequence entries, part 114.
197. gbest115.seq - EST (expressed sequence tag) sequence entries, part 115.
198. gbest116.seq - EST (expressed sequence tag) sequence entries, part 116.
199. gbest117.seq - EST (expressed sequence tag) sequence entries, part 117.
200. gbest118.seq - EST (expressed sequence tag) sequence entries, part 118.
201. gbest119.seq - EST (expressed sequence tag) sequence entries, part 119.
202. gbest120.seq - EST (expressed sequence tag) sequence entries, part 120.
203. gbest121.seq - EST (expressed sequence tag) sequence entries, part 121.
204. gbest122.seq - EST (expressed sequence tag) sequence entries, part 122.
205. gbest123.seq - EST (expressed sequence tag) sequence entries, part 123.
206. gbest124.seq - EST (expressed sequence tag) sequence entries, part 124.
207. gbest125.seq - EST (expressed sequence tag) sequence entries, part 125.
208. gbest126.seq - EST (expressed sequence tag) sequence entries, part 126.
209. gbest127.seq - EST (expressed sequence tag) sequence entries, part 127.
210. gbest128.seq - EST (expressed sequence tag) sequence entries, part 128.
211. gbest129.seq - EST (expressed sequence tag) sequence entries, part 129.
212. gbest130.seq - EST (expressed sequence tag) sequence entries, part 130.
213. gbest131.seq - EST (expressed sequence tag) sequence entries, part 131.
214. gbest132.seq - EST (expressed sequence tag) sequence entries, part 132.
215. gbest133.seq - EST (expressed sequence tag) sequence entries, part 133.
216. gbest134.seq - EST (expressed sequence tag) sequence entries, part 134.
217. gbest135.seq - EST (expressed sequence tag) sequence entries, part 135.
218. gbest136.seq - EST (expressed sequence tag) sequence entries, part 136.
219. gbest137.seq - EST (expressed sequence tag) sequence entries, part 137.
220. gbest138.seq - EST (expressed sequence tag) sequence entries, part 138.
221. gbest139.seq - EST (expressed sequence tag) sequence entries, part 139.
222. gbest140.seq - EST (expressed sequence tag) sequence entries, part 140.
223. gbest141.seq - EST (expressed sequence tag) sequence entries, part 141.
224. gbest142.seq - EST (expressed sequence tag) sequence entries, part 142.
225. gbest143.seq - EST (expressed sequence tag) sequence entries, part 143.
226. gbest144.seq - EST (expressed sequence tag) sequence entries, part 144.
227. gbest145.seq - EST (expressed sequence tag) sequence entries, part 145.
228. gbest146.seq - EST (expressed sequence tag) sequence entries, part 146.
229. gbest147.seq - EST (expressed sequence tag) sequence entries, part 147.
230. gbest148.seq - EST (expressed sequence tag) sequence entries, part 148.
231. gbest149.seq - EST (expressed sequence tag) sequence entries, part 149.
232. gbest150.seq - EST (expressed sequence tag) sequence entries, part 150.
233. gbest151.seq - EST (expressed sequence tag) sequence entries, part 151.
234. gbest152.seq - EST (expressed sequence tag) sequence entries, part 152.
235. gbest153.seq - EST (expressed sequence tag) sequence entries, part 153.
236. gbest154.seq - EST (expressed sequence tag) sequence entries, part 154.
237. gbest155.seq - EST (expressed sequence tag) sequence entries, part 155.
238. gbest156.seq - EST (expressed sequence tag) sequence entries, part 156.
239. gbest157.seq - EST (expressed sequence tag) sequence entries, part 157.
240. gbest158.seq - EST (expressed sequence tag) sequence entries, part 158.
241. gbest159.seq - EST (expressed sequence tag) sequence entries, part 159.
242. gbest160.seq - EST (expressed sequence tag) sequence entries, part 160.
243. gbest161.seq - EST (expressed sequence tag) sequence entries, part 161.
244. gbest162.seq - EST (expressed sequence tag) sequence entries, part 162.
245. gbest163.seq - EST (expressed sequence tag) sequence entries, part 163.
246. gbest164.seq - EST (expressed sequence tag) sequence entries, part 164.
247. gbest165.seq - EST (expressed sequence tag) sequence entries, part 165.
248. gbest166.seq - EST (expressed sequence tag) sequence entries, part 166.
249. gbest167.seq - EST (expressed sequence tag) sequence entries, part 167.
250. gbest168.seq - EST (expressed sequence tag) sequence entries, part 168.
251. gbest169.seq - EST (expressed sequence tag) sequence entries, part 169.
252. gbest170.seq - EST (expressed sequence tag) sequence entries, part 170.
253. gbest171.seq - EST (expressed sequence tag) sequence entries, part 171.
254. gbest172.seq - EST (expressed sequence tag) sequence entries, part 172.
255. gbest173.seq - EST (expressed sequence tag) sequence entries, part 173.
256. gbest174.seq - EST (expressed sequence tag) sequence entries, part 174.
257. gbest175.seq - EST (expressed sequence tag) sequence entries, part 175.
258. gbest176.seq - EST (expressed sequence tag) sequence entries, part 176.
259. gbest177.seq - EST (expressed sequence tag) sequence entries, part 177.
260. gbest178.seq - EST (expressed sequence tag) sequence entries, part 178.
261. gbest179.seq - EST (expressed sequence tag) sequence entries, part 179.
262. gbest180.seq - EST (expressed sequence tag) sequence entries, part 180.
263. gbest181.seq - EST (expressed sequence tag) sequence entries, part 181.
264. gbest182.seq - EST (expressed sequence tag) sequence entries, part 182.
265. gbest183.seq - EST (expressed sequence tag) sequence entries, part 183.
266. gbest184.seq - EST (expressed sequence tag) sequence entries, part 184.
267. gbest185.seq - EST (expressed sequence tag) sequence entries, part 185.
268. gbest186.seq - EST (expressed sequence tag) sequence entries, part 186.
269. gbest187.seq - EST (expressed sequence tag) sequence entries, part 187.
270. gbest188.seq - EST (expressed sequence tag) sequence entries, part 188.
271. gbest189.seq - EST (expressed sequence tag) sequence entries, part 189.
272. gbest190.seq - EST (expressed sequence tag) sequence entries, part 190.
273. gbest191.seq - EST (expressed sequence tag) sequence entries, part 191.
274. gbest192.seq - EST (expressed sequence tag) sequence entries, part 192.
275. gbest193.seq - EST (expressed sequence tag) sequence entries, part 193.
276. gbest194.seq - EST (expressed sequence tag) sequence entries, part 194.
277. gbest195.seq - EST (expressed sequence tag) sequence entries, part 195.
278. gbest196.seq - EST (expressed sequence tag) sequence entries, part 196.
279. gbest197.seq - EST (expressed sequence tag) sequence entries, part 197.
280. gbest198.seq - EST (expressed sequence tag) sequence entries, part 198.
281. gbest199.seq - EST (expressed sequence tag) sequence entries, part 199.
282. gbest200.seq - EST (expressed sequence tag) sequence entries, part 200.
283. gbest201.seq - EST (expressed sequence tag) sequence entries, part 201.
284. gbest202.seq - EST (expressed sequence tag) sequence entries, part 202.
285. gbest203.seq - EST (expressed sequence tag) sequence entries, part 203.
286. gbest204.seq - EST (expressed sequence tag) sequence entries, part 204.
287. gbest205.seq - EST (expressed sequence tag) sequence entries, part 205.
288. gbest206.seq - EST (expressed sequence tag) sequence entries, part 206.
289. gbest207.seq - EST (expressed sequence tag) sequence entries, part 207.
290. gbest208.seq - EST (expressed sequence tag) sequence entries, part 208.
291. gbest209.seq - EST (expressed sequence tag) sequence entries, part 209.
292. gbest210.seq - EST (expressed sequence tag) sequence entries, part 210.
293. gbest211.seq - EST (expressed sequence tag) sequence entries, part 211.
294. gbest212.seq - EST (expressed sequence tag) sequence entries, part 212.
295. gbest213.seq - EST (expressed sequence tag) sequence entries, part 213.
296. gbest214.seq - EST (expressed sequence tag) sequence entries, part 214.
297. gbest215.seq - EST (expressed sequence tag) sequence entries, part 215.
298. gbest216.seq - EST (expressed sequence tag) sequence entries, part 216.
299. gbest217.seq - EST (expressed sequence tag) sequence entries, part 217.
300. gbest218.seq - EST (expressed sequence tag) sequence entries, part 218.
301. gbest219.seq - EST (expressed sequence tag) sequence entries, part 219.
302. gbest220.seq - EST (expressed sequence tag) sequence entries, part 220.
303. gbest221.seq - EST (expressed sequence tag) sequence entries, part 221.
304. gbest222.seq - EST (expressed sequence tag) sequence entries, part 222.
305. gbest223.seq - EST (expressed sequence tag) sequence entries, part 223.
306. gbest224.seq - EST (expressed sequence tag) sequence entries, part 224.
307. gbest225.seq - EST (expressed sequence tag) sequence entries, part 225.
308. gbest226.seq - EST (expressed sequence tag) sequence entries, part 226.
309. gbest227.seq - EST (expressed sequence tag) sequence entries, part 227.
310. gbest228.seq - EST (expressed sequence tag) sequence entries, part 228.
311. gbest229.seq - EST (expressed sequence tag) sequence entries, part 229.
312. gbest230.seq - EST (expressed sequence tag) sequence entries, part 230.
313. gbest231.seq - EST (expressed sequence tag) sequence entries, part 231.
314. gbest232.seq - EST (expressed sequence tag) sequence entries, part 232.
315. gbest233.seq - EST (expressed sequence tag) sequence entries, part 233.
316. gbest234.seq - EST (expressed sequence tag) sequence entries, part 234.
317. gbest235.seq - EST (expressed sequence tag) sequence entries, part 235.
318. gbpat1.seq - Patent sequence entries, part 1.
319. gbpat2.seq - Patent sequence entries, part 2.
320. gbpat3.seq - Patent sequence entries, part 3.
321. gbpat4.seq - Patent sequence entries, part 4.
322. gbpat5.seq - Patent sequence entries, part 5.
323. gbpat6.seq - Patent sequence entries, part 6.
324. gbpat7.seq - Patent sequence entries, part 7.
325. gbsts1.seq - STS (sequence tagged site) sequence entries, part 1.
326. gbsts2.seq - STS (sequence tagged site) sequence entries, part 2.
327. gbgss1.seq - GSS (genome survey sequence) sequence entries, part 1.
328. gbgss2.seq - GSS (genome survey sequence) sequence entries, part 2.
329. gbgss3.seq - GSS (genome survey sequence) sequence entries, part 3.
330. gbgss4.seq - GSS (genome survey sequence) sequence entries, part 4.
331. gbgss5.seq - GSS (genome survey sequence) sequence entries, part 5.
332. gbgss6.seq - GSS (genome survey sequence) sequence entries, part 6.
333. gbgss7.seq - GSS (genome survey sequence) sequence entries, part 7.
334. gbgss8.seq - GSS (genome survey sequence) sequence entries, part 8.
335. gbgss9.seq - GSS (genome survey sequence) sequence entries, part 9.
336. gbgss10.seq - GSS (genome survey sequence) sequence entries, part 10.
337. gbgss11.seq - GSS (genome survey sequence) sequence entries, part 11.
338. gbgss12.seq - GSS (genome survey sequence) sequence entries, part 12.
339. gbgss13.seq - GSS (genome survey sequence) sequence entries, part 13.
340. gbgss14.seq - GSS (genome survey sequence) sequence entries, part 14.
341. gbgss15.seq - GSS (genome survey sequence) sequence entries, part 15.
342. gbgss16.seq - GSS (genome survey sequence) sequence entries, part 16.
343. gbgss17.seq - GSS (genome survey sequence) sequence entries, part 17.
344. gbgss18.seq - GSS (genome survey sequence) sequence entries, part 18.
345. gbgss19.seq - GSS (genome survey sequence) sequence entries, part 19.
346. gbgss20.seq - GSS (genome survey sequence) sequence entries, part 20.
347. gbgss21.seq - GSS (genome survey sequence) sequence entries, part 21.
348. gbgss22.seq - GSS (genome survey sequence) sequence entries, part 22.
349. gbgss23.seq - GSS (genome survey sequence) sequence entries, part 23.
350. gbgss24.seq - GSS (genome survey sequence) sequence entries, part 24.
351. gbgss25.seq - GSS (genome survey sequence) sequence entries, part 25.
352. gbgss26.seq - GSS (genome survey sequence) sequence entries, part 26.
353. gbgss27.seq - GSS (genome survey sequence) sequence entries, part 27.
354. gbgss28.seq - GSS (genome survey sequence) sequence entries, part 28.
355. gbgss29.seq - GSS (genome survey sequence) sequence entries, part 29.
356. gbgss30.seq - GSS (genome survey sequence) sequence entries, part 30.
357. gbgss31.seq - GSS (genome survey sequence) sequence entries, part 31.
358. gbgss32.seq - GSS (genome survey sequence) sequence entries, part 32.
359. gbgss33.seq - GSS (genome survey sequence) sequence entries, part 33.
360. gbgss34.seq - GSS (genome survey sequence) sequence entries, part 34.
361. gbgss35.seq - GSS (genome survey sequence) sequence entries, part 35.
362. gbgss36.seq - GSS (genome survey sequence) sequence entries, part 36.
363. gbgss37.seq - GSS (genome survey sequence) sequence entries, part 37.
364. gbgss38.seq - GSS (genome survey sequence) sequence entries, part 38.
365. gbgss39.seq - GSS (genome survey sequence) sequence entries, part 39.
366. gbgss40.seq - GSS (genome survey sequence) sequence entries, part 40.
367. gbgss41.seq - GSS (genome survey sequence) sequence entries, part 41.
368. gbgss42.seq - GSS (genome survey sequence) sequence entries, part 42.
369. gbgss43.seq - GSS (genome survey sequence) sequence entries, part 43.
370. gbgss44.seq - GSS (genome survey sequence) sequence entries, part 44.
371. gbgss45.seq - GSS (genome survey sequence) sequence entries, part 45.
372. gbgss46.seq - GSS (genome survey sequence) sequence entries, part 46.
373. gbgss47.seq - GSS (genome survey sequence) sequence entries, part 47.
374. gbgss48.seq - GSS (genome survey sequence) sequence entries, part 48.
375. gbgss49.seq - GSS (genome survey sequence) sequence entries, part 49.
376. gbgss50.seq - GSS (genome survey sequence) sequence entries, part 50.
377. gbgss51.seq - GSS (genome survey sequence) sequence entries, part 51.
378. gbgss52.seq - GSS (genome survey sequence) sequence entries, part 52.
379. gbgss53.seq - GSS (genome survey sequence) sequence entries, part 53.
380. gbgss54.seq - GSS (genome survey sequence) sequence entries, part 54.
381. gbgss55.seq - GSS (genome survey sequence) sequence entries, part 55.
382. gbgss56.seq - GSS (genome survey sequence) sequence entries, part 56.
383. gbgss57.seq - GSS (genome survey sequence) sequence entries, part 57.
384. gbgss58.seq - GSS (genome survey sequence) sequence entries, part 58.
385. gbgss59.seq - GSS (genome survey sequence) sequence entries, part 59.
386. gbgss60.seq - GSS (genome survey sequence) sequence entries, part 60.
387. gbgss61.seq - GSS (genome survey sequence) sequence entries, part 61.
388. gbgss62.seq - GSS (genome survey sequence) sequence entries, part 62.
389. gbgss63.seq - GSS (genome survey sequence) sequence entries, part 63.
390. gbhtg1.seq - HTGS (high throughput genomic sequencing) sequence entries, part 1.
391. gbhtg2.seq - HTGS (high throughput genomic sequencing) sequence entries, part 2.
392. gbhtg3.seq - HTGS (high throughput genomic sequencing) sequence entries, part 3.
393. gbhtg4.seq - HTGS (high throughput genomic sequencing) sequence entries, part 4.
394. gbhtg5.seq - HTGS (high throughput genomic sequencing) sequence entries, part 5.
395. gbhtg6.seq - HTGS (high throughput genomic sequencing) sequence entries, part 6.
396. gbhtg7.seq - HTGS (high throughput genomic sequencing) sequence entries, part 7.
397. gbhtg8.seq - HTGS (high throughput genomic sequencing) sequence entries, part 8.
398. gbhtg9.seq - HTGS (high throughput genomic sequencing) sequence entries, part 9.
399. gbhtg10.seq - HTGS (high throughput genomic sequencing) sequence entries, part 10.
400. gbhtg11.seq - HTGS (high throughput genomic sequencing) sequence entries, part 11.
401. gbhtg12.seq - HTGS (high throughput genomic sequencing) sequence entries, part 12.
402. gbhtg13.seq - HTGS (high throughput genomic sequencing) sequence entries, part 13.
403. gbhtg14.seq - HTGS (high throughput genomic sequencing) sequence entries, part 14.
404. gbhtg15.seq - HTGS (high throughput genomic sequencing) sequence entries, part 15.
405. gbhtg16.seq - HTGS (high throughput genomic sequencing) sequence entries, part 16.
406. gbhtg17.seq - HTGS (high throughput genomic sequencing) sequence entries, part 17.
407. gbhtg18.seq - HTGS (high throughput genomic sequencing) sequence entries, part 18.
408. gbhtg19.seq - HTGS (high throughput genomic sequencing) sequence entries, part 19.
409. gbhtg20.seq - HTGS (high throughput genomic sequencing) sequence entries, part 20.
410. gbhtg21.seq - HTGS (high throughput genomic sequencing) sequence entries, part 21.
411. gbhtg22.seq - HTGS (high throughput genomic sequencing) sequence entries, part 22.
412. gbhtg23.seq - HTGS (high throughput genomic sequencing) sequence entries, part 23.
413. gbhtg24.seq - HTGS (high throughput genomic sequencing) sequence entries, part 24.
414. gbhtg25.seq - HTGS (high throughput genomic sequencing) sequence entries, part 25.
415. gbhtg26.seq - HTGS (high throughput genomic sequencing) sequence entries, part 26.
416. gbhtg27.seq - HTGS (high throughput genomic sequencing) sequence entries, part 27.
417. gbhtg28.seq - HTGS (high throughput genomic sequencing) sequence entries, part 28.
418. gbhtg29.seq - HTGS (high throughput genomic sequencing) sequence entries, part 29.
419. gbhtg30.seq - HTGS (high throughput genomic sequencing) sequence entries, part 30.
420. gbhtg31.seq - HTGS (high throughput genomic sequencing) sequence entries, part 31.
421. gbhtg32.seq - HTGS (high throughput genomic sequencing) sequence entries, part 32.
422. gbhtg33.seq - HTGS (high throughput genomic sequencing) sequence entries, part 33.
423. gbhtg34.seq - HTGS (high throughput genomic sequencing) sequence entries, part 34.
424. gbhtg35.seq - HTGS (high throughput genomic sequencing) sequence entries, part 35.
425. gbhtg36.seq - HTGS (high throughput genomic sequencing) sequence entries, part 36.
426. gbhtg37.seq - HTGS (high throughput genomic sequencing) sequence entries, part 37.
427. gbhtg38.seq - HTGS (high throughput genomic sequencing) sequence entries, part 38.
428. gbhtg39.seq - HTGS (high throughput genomic sequencing) sequence entries, part 39.
429. gbhtg40.seq - HTGS (high throughput genomic sequencing) sequence entries, part 40.
430. gbhtg41.seq - HTGS (high throughput genomic sequencing) sequence entries, part 41.
431. gbhtg42.seq - HTGS (high throughput genomic sequencing) sequence entries, part 42.
432. gbhtg43.seq - HTGS (high throughput genomic sequencing) sequence entries, part 43.
433. gbhtg44.seq - HTGS (high throughput genomic sequencing) sequence entries, part 44.
434. gbhtg45.seq - HTGS (high throughput genomic sequencing) sequence entries, part 45.
435. gbhtg46.seq - HTGS (high throughput genomic sequencing) sequence entries, part 46.
436. gbhtg47.seq - HTGS (high throughput genomic sequencing) sequence entries, part 47.
437. gbhtg48.seq - HTGS (high throughput genomic sequencing) sequence entries, part 48.
438. gbhtg49.seq - HTGS (high throughput genomic sequencing) sequence entries, part 49.
439. gbhtg50.seq - HTGS (high throughput genomic sequencing) sequence entries, part 50.
440. gbhtg51.seq - HTGS (high throughput genomic sequencing) sequence entries, part 51.
441. gbhtg52.seq - HTGS (high throughput genomic sequencing) sequence entries, part 52.
442. gbhtg53.seq - HTGS (high throughput genomic sequencing) sequence entries, part 53.
443. gbhtg54.seq - HTGS (high throughput genomic sequencing) sequence entries, part 54.
444. gbhtg55.seq - HTGS (high throughput genomic sequencing) sequence entries, part 55.
445. gbhtg56.seq - HTGS (high throughput genomic sequencing) sequence entries, part 56.
446. gbhtg57.seq - HTGS (high throughput genomic sequencing) sequence entries, part 57.
447. gbhtc1.seq - HTC (high throughput cDNA sequencing) entries, part 1.
448. gbhtc2.seq - HTC (high throughput cDNA sequencing) entries, part 2.
449. gbhtc3.seq - HTC (high throughput cDNA sequencing) entries, part 3.
Three Supplemental files provide the accession numbers of GenBank entries
that are new, updated, or deleted since the previous release:
a. gbchg.txt - Entries updated since the previous release.
b. gbdel.txt - Entries deleted since the previous release.
c. gbnew.txt - Entries new since the previous release.
An experimental file called gbcon.seq provides an alternative representation
for complex sequences, such as "segmented sets" and complete-genomes that have
been split into pieces. The GenBank README describes the experimental CON
division of GenBank in more detail:
ftp://ftp.ncbi.nih.gov/genbank/README.genbank
2.2.5 File Sizes
Uncompressed, the Release 133.0 flatfiles require roughly 94.33 GB (sequence
files only) or 107.07 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
729063968 gbacc.idx
502265875 gbaut1.idx
501503933 gbaut10.idx
501489761 gbaut11.idx
505671078 gbaut12.idx
516521192 gbaut13.idx
504423074 gbaut14.idx
511905025 gbaut15.idx
501827134 gbaut16.idx
506962319 gbaut17.idx
459196711 gbaut18.idx
500012393 gbaut2.idx
504522507 gbaut3.idx
516903974 gbaut4.idx
514663509 gbaut5.idx
505091071 gbaut6.idx
500083130 gbaut7.idx
500034204 gbaut8.idx
529808973 gbaut9.idx
250008897 gbbct1.seq
250000679 gbbct2.seq
250367557 gbbct3.seq
250026652 gbbct4.seq
250005433 gbbct5.seq
128435234 gbbct6.seq
1954012 gbchg.txt
313833 gbdel.txt
230687688 gbest1.seq
230688999 gbest10.seq
230689470 gbest100.seq
230689391 gbest101.seq
230689273 gbest102.seq
230689008 gbest103.seq
230689710 gbest104.seq
230688510 gbest105.seq
230689148 gbest106.seq
230687855 gbest107.seq
230689348 gbest108.seq
230691072 gbest109.seq
230687854 gbest11.seq
230688197 gbest110.seq
230689388 gbest111.seq
230690390 gbest112.seq
230688682 gbest113.seq
230689993 gbest114.seq
230690611 gbest115.seq
230688742 gbest116.seq
230687584 gbest117.seq
230687811 gbest118.seq
230689803 gbest119.seq
230689601 gbest12.seq
230688335 gbest120.seq
230688709 gbest121.seq
230689693 gbest122.seq
230688953 gbest123.seq
230689190 gbest124.seq
230688951 gbest125.seq
230687785 gbest126.seq
230689527 gbest127.seq
230688807 gbest128.seq
230689739 gbest129.seq
230687861 gbest13.seq
230688465 gbest130.seq
230690530 gbest131.seq
230688491 gbest132.seq
230688317 gbest133.seq
230689672 gbest134.seq
230689590 gbest135.seq
230688478 gbest136.seq
230688223 gbest137.seq
230690482 gbest138.seq
230690139 gbest139.seq
230687867 gbest14.seq
230689541 gbest140.seq
230688661 gbest141.seq
230687631 gbest142.seq
230689282 gbest143.seq
230689007 gbest144.seq
230687676 gbest145.seq
230692318 gbest146.seq
230689646 gbest147.seq
230688820 gbest148.seq
230690162 gbest149.seq
230687708 gbest15.seq
230689355 gbest150.seq
230689888 gbest151.seq
230689873 gbest152.seq
230690306 gbest153.seq
230687874 gbest154.seq
230690602 gbest155.seq
230688767 gbest156.seq
230688892 gbest157.seq
230689732 gbest158.seq
230689493 gbest159.seq
230687480 gbest16.seq
230694518 gbest160.seq
230687830 gbest161.seq
230688865 gbest162.seq
230689027 gbest163.seq
230687777 gbest164.seq
230689231 gbest165.seq
230688944 gbest166.seq
230688866 gbest167.seq
230689418 gbest168.seq
230689661 gbest169.seq
230688694 gbest17.seq
230688687 gbest170.seq
230689463 gbest171.seq
230688474 gbest172.seq
230689490 gbest173.seq
230687808 gbest174.seq
230687992 gbest175.seq
230688684 gbest176.seq
230689652 gbest177.seq
230690825 gbest178.seq
230689087 gbest179.seq
230689477 gbest18.seq
230690381 gbest180.seq
230689659 gbest181.seq
230690066 gbest182.seq
230688606 gbest183.seq
230689483 gbest184.seq
230688577 gbest185.seq
230689321 gbest186.seq
230689094 gbest187.seq
230688740 gbest188.seq
166704146 gbest189.seq
230689351 gbest19.seq
163151684 gbest190.seq
167375148 gbest191.seq
172134552 gbest192.seq
170860362 gbest193.seq
166619818 gbest194.seq
166514436 gbest195.seq
166408389 gbest196.seq
167104595 gbest197.seq
167450525 gbest198.seq
166974019 gbest199.seq
230690037 gbest2.seq
230688393 gbest20.seq
174274473 gbest200.seq
162982949 gbest201.seq
173127622 gbest202.seq
163873046 gbest203.seq
164747197 gbest204.seq
169607771 gbest205.seq
171933736 gbest206.seq
168597639 gbest207.seq
166620886 gbest208.seq
167137712 gbest209.seq
230691374 gbest21.seq
167253197 gbest210.seq
168239573 gbest211.seq
167085304 gbest212.seq
166535785 gbest213.seq
176538728 gbest214.seq
181779763 gbest215.seq
177274776 gbest216.seq
194122855 gbest217.seq
230688542 gbest218.seq
230687910 gbest219.seq
230689091 gbest22.seq
230690008 gbest220.seq
230688799 gbest221.seq
230688568 gbest222.seq
230689135 gbest223.seq
230689385 gbest224.seq
230688453 gbest225.seq
230688017 gbest226.seq
230687758 gbest227.seq
230688889 gbest228.seq
230689865 gbest229.seq
230687783 gbest23.seq
230689205 gbest230.seq
230690142 gbest231.seq
230687885 gbest232.seq
227443835 gbest233.seq
230689017 gbest234.seq
118538965 gbest235.seq
230689292 gbest24.seq
230690112 gbest25.seq
230690594 gbest26.seq
230687556 gbest27.seq
230689345 gbest28.seq
230689877 gbest29.seq
230688556 gbest3.seq
230688166 gbest30.seq
230688174 gbest31.seq
230688457 gbest32.seq
230688108 gbest33.seq
230687970 gbest34.seq
230687635 gbest35.seq
211054287 gbest36.seq
210079554 gbest37.seq
210664900 gbest38.seq
217981580 gbest39.seq
230689798 gbest4.seq
216550231 gbest40.seq
216342030 gbest41.seq
217283558 gbest42.seq
230687911 gbest43.seq
230689536 gbest44.seq
221834636 gbest45.seq
230689696 gbest46.seq
230687802 gbest47.seq
230687760 gbest48.seq
230689313 gbest49.seq
165267638 gbest5.seq
230690123 gbest50.seq
230689502 gbest51.seq
230689047 gbest52.seq
230688012 gbest53.seq
230689817 gbest54.seq
230690661 gbest55.seq
230688056 gbest56.seq
230689186 gbest57.seq
230687916 gbest58.seq
230687464 gbest59.seq
180014575 gbest6.seq
230690475 gbest60.seq
230689386 gbest61.seq
209862458 gbest62.seq
209376586 gbest63.seq
208935191 gbest64.seq
209219447 gbest65.seq
210511396 gbest66.seq
209974961 gbest67.seq
208802147 gbest68.seq
209485067 gbest69.seq
230687546 gbest7.seq
210666005 gbest70.seq
206520828 gbest71.seq
206847410 gbest72.seq
208276982 gbest73.seq
208696492 gbest74.seq
215665447 gbest75.seq
230690130 gbest76.seq
230689783 gbest77.seq
230687473 gbest78.seq
227513684 gbest79.seq
230689515 gbest8.seq
217362692 gbest80.seq
219203234 gbest81.seq
230687684 gbest82.seq
230689130 gbest83.seq
230688750 gbest84.seq
230690568 gbest85.seq
230688307 gbest86.seq
230688975 gbest87.seq
230688447 gbest88.seq
230690211 gbest89.seq
230687748 gbest9.seq
230689603 gbest90.seq
230687503 gbest91.seq
230691964 gbest92.seq
230690331 gbest93.seq
230687572 gbest94.seq
230687976 gbest95.seq
230688808 gbest96.seq
230690865 gbest97.seq
230690710 gbest98.seq
230689195 gbest99.seq
27852020 gbgen.idx
209717500 gbgss1.seq
209716794 gbgss10.seq
209718369 gbgss11.seq
209719058 gbgss12.seq
209717684 gbgss13.seq
209718195 gbgss14.seq
209718460 gbgss15.seq
209719508 gbgss16.seq
209717619 gbgss17.seq
209718699 gbgss18.seq
209715982 gbgss19.seq
209717920 gbgss2.seq
209718113 gbgss20.seq
209719545 gbgss21.seq
209719231 gbgss22.seq
209716350 gbgss23.seq
209720092 gbgss24.seq
209717151 gbgss25.seq
209717784 gbgss26.seq
209718015 gbgss27.seq
209717394 gbgss28.seq
209718013 gbgss29.seq
209717432 gbgss3.seq
209718476 gbgss30.seq
209717160 gbgss31.seq
209716069 gbgss32.seq
209716912 gbgss33.seq
209718075 gbgss34.seq
209717155 gbgss35.seq
209716093 gbgss36.seq
209718669 gbgss37.seq
209716177 gbgss38.seq
209716587 gbgss39.seq
209717295 gbgss4.seq
209715922 gbgss40.seq
209717142 gbgss41.seq
209718051 gbgss42.seq
209716739 gbgss43.seq
209717788 gbgss44.seq
209717661 gbgss45.seq
209717795 gbgss46.seq
209718859 gbgss47.seq
209719251 gbgss48.seq
209715955 gbgss49.seq
209717368 gbgss5.seq
209717878 gbgss50.seq
209716430 gbgss51.seq
209717961 gbgss52.seq
209717000 gbgss53.seq
28953412 gbgss54.seq
250002498 gbgss55.seq
250001772 gbgss56.seq
250000388 gbgss57.seq
250000601 gbgss58.seq
250000632 gbgss59.seq
209717060 gbgss6.seq
250002763 gbgss60.seq
250001602 gbgss61.seq
250001817 gbgss62.seq
234319985 gbgss63.seq
209718308 gbgss7.seq
209718139 gbgss8.seq
209717651 gbgss9.seq
250008469 gbhtc1.seq
250004233 gbhtc2.seq
159495870 gbhtc3.seq
250002199 gbhtg1.seq
250202194 gbhtg10.seq
250132762 gbhtg11.seq
250128666 gbhtg12.seq
250147000 gbhtg13.seq
250276523 gbhtg14.seq
250089994 gbhtg15.seq
250037960 gbhtg16.seq
250067038 gbhtg17.seq
250082700 gbhtg18.seq
250147277 gbhtg19.seq
250104522 gbhtg2.seq
250014725 gbhtg20.seq
250006180 gbhtg21.seq
250123662 gbhtg22.seq
250082425 gbhtg23.seq
250170147 gbhtg24.seq
250119188 gbhtg25.seq
250142454 gbhtg26.seq
250004229 gbhtg27.seq
250242159 gbhtg28.seq
250104466 gbhtg29.seq
250023951 gbhtg3.seq
250045176 gbhtg30.seq
250232415 gbhtg31.seq
250140400 gbhtg32.seq
250077912 gbhtg33.seq
250241226 gbhtg34.seq
250094081 gbhtg35.seq
250246540 gbhtg36.seq
250060783 gbhtg37.seq
250205323 gbhtg38.seq
250311103 gbhtg39.seq
250060829 gbhtg4.seq
250099351 gbhtg40.seq
250181662 gbhtg41.seq
250028706 gbhtg42.seq
250354925 gbhtg43.seq
250084441 gbhtg44.seq
250263973 gbhtg45.seq
250004197 gbhtg46.seq
250002032 gbhtg47.seq
250070034 gbhtg48.seq
250125216 gbhtg49.seq
250026311 gbhtg5.seq
250011666 gbhtg50.seq
250087427 gbhtg51.seq
250026385 gbhtg52.seq
250049681 gbhtg53.seq
250100598 gbhtg54.seq
250187898 gbhtg55.seq
250077328 gbhtg56.seq
90081335 gbhtg57.seq
250066041 gbhtg6.seq
250215886 gbhtg7.seq
250176755 gbhtg8.seq
250227386 gbhtg9.seq
250083066 gbinv1.seq
250096964 gbinv2.seq
250000693 gbinv3.seq
250017622 gbinv4.seq
216601588 gbinv5.seq
559233299 gbjou.idx
502549211 gbkey.idx
150243349 gbmam.seq
39797694 gbnew.txt
250000474 gbpat1.seq
250000831 gbpat2.seq
250137890 gbpat3.seq
250003014 gbpat4.seq
250003170 gbpat5.seq
250000325 gbpat6.seq
12736517 gbpat7.seq
19556999 gbphg.seq
250043518 gbpln1.seq
250000648 gbpln2.seq
250184383 gbpln3.seq
250005885 gbpln4.seq
250001047 gbpln5.seq
250001465 gbpln6.seq
47594260 gbpln7.seq
250041351 gbpri1.seq
250047051 gbpri10.seq
250174588 gbpri11.seq
250097660 gbpri12.seq
250001108 gbpri13.seq
250002143 gbpri14.seq
250070030 gbpri15.seq
250198384 gbpri16.seq
250003366 gbpri17.seq
250098312 gbpri18.seq
250108669 gbpri19.seq
250191080 gbpri2.seq
250008370 gbpri20.seq
250042782 gbpri21.seq
250067175 gbpri22.seq
250003891 gbpri23.seq
102620129 gbpri24.seq
250143759 gbpri3.seq
250108436 gbpri4.seq
250028000 gbpri5.seq
250280745 gbpri6.seq
250056061 gbpri7.seq
250216691 gbpri8.seq
250206323 gbpri9.seq
147334 gbrel.txt
250192343 gbrod1.seq
250084794 gbrod2.seq
250235678 gbrod3.seq
250013880 gbrod4.seq
250000420 gbrod5.seq
101447374 gbrod6.seq
1785538677 gbsdr.txt
1461004 gbsec.idx
250001708 gbsts1.seq
172710085 gbsts2.seq
34094288 gbsyn.seq
1417399 gbuna.seq
250001373 gbvrl1.seq
250001140 gbvrl2.seq
80136039 gbvrl3.seq
250015830 gbvrt1.seq
115201812 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 20909 102678263
BCT2 8857 106684010
BCT3 64413 87886582
BCT4 17166 106777490
BCT5 39191 95157045
BCT6 20595 46419783
EST1 68333 26365039
EST10 76745 29941526
EST100 71828 32887395
EST101 70445 30012313
EST102 66150 37311305
EST103 69249 37063950
EST104 68395 44346090
EST105 73527 33098409
EST106 75506 34919781
EST107 74832 27279714
EST108 73941 35762983
EST109 73697 35569915
EST11 75365 28764290
EST110 69992 42352086
EST111 80607 44516389
EST112 77034 46494948
EST113 69206 43346193
EST114 67465 43009589
EST115 74565 50174447
EST116 70242 42772133
EST117 75480 43579292
EST118 73390 46267488
EST119 72076 47859615
EST12 77514 30859409
EST120 74068 51620744
EST121 79083 39372138
EST122 76134 30964750
EST123 79147 40507047
EST124 78363 42581744
EST125 76712 47610042
EST126 60764 28087582
EST127 74757 42122989
EST128 68367 37229353
EST129 67867 38861410
EST13 77206 29188394
EST130 71302 42291782
EST131 73515 47651805
EST132 66820 38870075
EST133 73471 41676219
EST134 69013 40180569
EST135 60632 37420261
EST136 88693 48005885
EST137 93083 52892284
EST138 71948 37670770
EST139 72857 38604876
EST14 78691 31973028
EST140 95997 51092712
EST141 103695 56605904
EST142 93549 54238908
EST143 69498 39870838
EST144 66570 31714694
EST145 62164 29403250
EST146 57506 30282336
EST147 62910 31147774
EST148 53850 27207550
EST149 80774 56103456
EST15 73822 31221266
EST150 68988 37254494
EST151 73355 51659695
EST152 70790 39959795
EST153 61444 30687607
EST154 64952 39968182
EST155 68228 31162165
EST156 63406 46797205
EST157 70947 40042043
EST158 68688 41495981
EST159 68522 40839718
EST16 75556 33225382
EST160 62211 36273436
EST161 66764 43105040
EST162 68794 30390360
EST163 76867 33307211
EST164 69246 43264111
EST165 74729 36902989
EST166 66765 34940828
EST167 71064 51435701
EST168 68182 45551581
EST169 68767 35025125
EST17 83282 34236589
EST170 69468 47372358
EST171 69307 51545638
EST172 69583 36587190
EST173 70896 44365006
EST174 70960 60306434
EST175 64114 47110110
EST176 63539 47027266
EST177 63865 46419695
EST178 65274 45874735
EST179 67030 51643869
EST18 80498 32259338
EST180 63023 39914016
EST181 64309 38317377
EST182 59375 32898366
EST183 74819 39787698
EST184 84416 55179721
EST185 69202 41504038
EST186 104547 66007395
EST187 107299 64796337
EST188 108403 64203205
EST189 27303 10067575
EST19 78881 32363613
EST190 27794 10578726
EST191 27093 10046898
EST192 26279 9589385
EST193 26553 8973600
EST194 27141 9910421
EST195 27056 9772580
EST196 26976 9707078
EST197 26896 10507259
EST198 26711 11766957
EST199 26807 10982846
EST2 75036 28805559
EST20 74330 30142776
EST200 25736 9443732
EST201 27749 9305572
EST202 26100 9001127
EST203 27647 11257981
EST204 27548 10725992
EST205 26706 11201486
EST206 26088 11710806
EST207 26652 11184028
EST208 26999 10880037
EST209 26794 11414071
EST21 73733 34275961
EST210 26880 11447312
EST211 26688 10955703
EST212 26846 10634377
EST213 27011 10549864
EST214 25326 10019072
EST215 24358 16138446
EST216 25091 16603509
EST217 51582 23878843
EST218 95127 39811215
EST219 70839 41390389
EST22 75862 30433067
EST220 81304 46575024
EST221 63943 46216351
EST222 66098 37385388
EST223 70229 36187848
EST224 101685 46641206
EST225 79371 44178301
EST226 65671 33970785
EST227 76482 34071430
EST228 92306 29968899
EST229 69938 24887145
EST23 77239 32321013
EST230 73772 27737942
EST231 74241 26168513
EST232 78742 27134951
EST233 73954 26554339
EST234 69351 29496370
EST235 41315 14463209
EST24 75445 33738037
EST25 72304 30715455
EST26 76178 31658232
EST27 76268 33171930
EST28 103510 49521499
EST29 70699 46219557
EST3 73894 29981502
EST30 82306 56263044
EST31 91666 50506414
EST32 97277 50215845
EST33 93812 43645473
EST34 93990 49082163
EST35 100451 45108702
EST36 60024 17289786
EST37 59603 15776911
EST38 60426 16206926
EST39 59509 18234177
EST4 74402 28251763
EST40 43563 11907360
EST41 43149 11862894
EST42 43062 11390523
EST43 83692 34977200
EST44 95572 43492640
EST45 89672 47075721
EST46 84734 39578750
EST47 107095 56564239
EST48 93786 45491123
EST49 76068 32418168
EST5 48500 15380287
EST50 68444 30193462
EST51 71129 30821176
EST52 72311 30266401
EST53 83359 33681671
EST54 74056 29176735
EST55 64880 28102513
EST56 70471 31036961
EST57 76908 36569563
EST58 73838 32330375
EST59 75111 27277246
EST6 55669 17851521
EST60 79431 30225671
EST61 74096 32935019
EST62 40205 11461834
EST63 40188 11292002
EST64 40336 12660891
EST65 40621 12295843
EST66 40602 12462886
EST67 40506 12941905
EST68 40519 12576532
EST69 40350 12103904
EST7 74567 29348606
EST70 40359 12336423
EST71 41180 12272642
EST72 41306 12384589
EST73 41225 13109266
EST74 41026 13015813
EST75 43663 12487989
EST76 43433 20114254
EST77 40594 24563775
EST78 42767 18443474
EST79 44600 18735226
EST8 76202 30681145
EST80 49658 21334919
EST81 48788 20995216
EST82 69627 31621387
EST83 72905 27836636
EST84 74528 29301210
EST85 75399 41588448
EST86 78340 40961592
EST87 76519 43608275
EST88 77507 35337289
EST89 74306 43365142
EST9 77738 29969805
EST90 72075 36685511
EST91 73933 38294179
EST92 72962 38729562
EST93 75778 42124724
EST94 70353 40531945
EST95 69361 36349005
EST96 73344 35497824
EST97 72664 47395996
EST98 72181 43985099
EST99 71807 42807997
GSS1 83286 35682444
GSS10 66628 34170349
GSS11 68874 40613150
GSS12 62891 31915603
GSS13 65573 34559166
GSS14 69194 36072590
GSS15 65572 29702574
GSS16 64454 29759069
GSS17 71546 41744414
GSS18 65572 33893159
GSS19 60258 27417835
GSS2 83477 35629691
GSS20 52121 27248219
GSS21 52559 26107903
GSS22 53721 23103306
GSS23 57867 33370620
GSS24 58830 30392137
GSS25 52942 25070913
GSS26 60543 39580044
GSS27 64369 27373566
GSS28 54059 22156781
GSS29 55485 27567056
GSS3 81443 38312715
GSS30 66670 31556204
GSS31 55449 31976170
GSS32 85570 38076376
GSS33 69642 36866420
GSS34 67989 38936583
GSS35 64914 41665671
GSS36 73317 35921632
GSS37 70020 37051488
GSS38 71528 37974521
GSS39 85924 56344940
GSS4 74353 38119884
GSS40 85999 57118206
GSS41 80947 42000763
GSS42 84521 50742390
GSS43 79212 35227839
GSS44 76365 28798680
GSS45 74330 48365492
GSS46 74147 52339234
GSS47 69179 48198592
GSS48 66236 43925435
GSS49 66370 43660710
GSS5 71182 38066855
GSS50 72664 40097502
GSS51 73011 37336501
GSS52 82211 59029622
GSS53 79225 65395756
GSS54 10228 3533948
GSS55 88062 66597557
GSS56 84358 63376892
GSS57 95582 37385608
GSS58 82247 62935677
GSS59 70619 59121013
GSS6 70634 35405867
GSS60 70168 58974706
GSS61 65243 63314312
GSS62 84103 56241726
GSS63 99537 45753168
GSS7 70945 35613804
GSS8 71352 36474544
GSS9 68975 34298841
HTC1 27605 44414413
HTC2 25937 58769348
HTC3 29047 45650610
HTG1 1328 190652500
HTG10 1145 190377480
HTG11 1546 186385982
HTG12 1047 191853300
HTG13 734 192539642
HTG14 731 192779864
HTG15 732 192449744
HTG16 791 192458352
HTG17 740 192544473
HTG18 759 192597834
HTG19 2055 179022636
HTG2 2056 188399975
HTG20 1257 186732197
HTG21 972 190212361
HTG22 1166 189133571
HTG23 747 192447192
HTG24 932 190891461
HTG25 969 190446741
HTG26 937 191020786
HTG27 876 191159018
HTG28 771 192516814
HTG29 987 190453380
HTG3 2617 187670821
HTG30 847 191645917
HTG31 974 190779344
HTG32 1135 188692262
HTG33 1045 189778956
HTG34 1059 189938444
HTG35 1109 189101582
HTG36 1051 190204056
HTG37 928 192159862
HTG38 1166 189546890
HTG39 990 191613394
HTG4 2895 189904440
HTG40 915 191816267
HTG41 878 192468271
HTG42 838 191947191
HTG43 907 191773867
HTG44 999 190863781
HTG45 987 191348098
HTG46 966 191700065
HTG47 1046 190569359
HTG48 1134 190226933
HTG49 1223 189589523
HTG5 1283 188492918
HTG50 1162 189969384
HTG51 1446 189022564
HTG52 1060 193336432
HTG53 1002 194024174
HTG54 1141 191038940
HTG55 1359 194222678
HTG56 1201 192675923
HTG57 372 65030971
HTG6 1291 187703093
HTG7 1242 188508008
HTG8 1254 188098048
HTG9 1273 188609476
INV1 8899 175299354
INV2 1868 165480545
INV3 63781 87212007
INV4 40330 105083221
INV5 35768 92577491
MAM 44517 51377750
PAT1 222798 70208547
PAT2 164817 89779309
PAT3 143470 91004073
PAT4 117436 112343126
PAT5 131364 59742530
PAT6 144124 59991209
PAT7 13338 3054369
PHG 2241 7457849
PLN1 18358 141980521
PLN2 72446 87139166
PLN3 42872 116786186
PLN4 35683 110795411
PLN5 55267 80094320
PLN6 40467 112628634
PLN7 11076 17650439
PRI1 13599 155620524
PRI10 1345 173839918
PRI11 1318 176421078
PRI12 1579 176723848
PRI13 11603 164263952
PRI14 42896 117337468
PRI15 13700 154776988
PRI16 1590 180042900
PRI17 1748 181169911
PRI18 2226 187564295
PRI19 1450 186293023
PRI2 1422 173803916
PRI20 28733 131822634
PRI21 17339 154293397
PRI22 47472 117916209
PRI23 37035 125378837
PRI24 28939 34220185
PRI3 1259 182669656
PRI4 1266 177079910
PRI5 1138 173940204
PRI6 1242 181412610
PRI7 1194 174143519
PRI8 1300 169141719
PRI9 1274 177619083
ROD1 6543 180396688
ROD2 22998 157088397
ROD3 1168 194415880
ROD4 1221 194497124
ROD5 33686 129372311
ROD6 28448 33488413
STS1 89972 35652835
STS2 66087 30459843
SYN 7665 13852062
UNA 612 330831
VRL1 74162 63822434
VRL2 78362 61636850
VRL3 18833 27503541
VRT1 56005 106201853
VRT2 35322 34526315
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 133.0 (chloroplast and mitochon-
drial sequences not included):
Entries Bases Species
6360016 9392891274 Homo sapiens
658937 5380664060 Rattus norvegicus
4772153 5292468980 Mus musculus
345914 691618258 Drosophila melanogaster
167440 577585512 Oryza sativa (japonica cultivar-group)
334671 444851980 Danio rerio
567852 386342341 Brassica oleracea
448420 374911466 Arabidopsis thaliana
401998 298912387 Gallus gallus
499168 294074230 Ciona intestinalis
450819 222535093 Zea mays
196555 220325190 Caenorhabditis elegans
418028 207346955 Triticum aestivum
189149 170126319 Tetraodon nigroviridis
160980 169390455 Pan troglodytes
282022 156113711 Hordeum vulgare subsp. vulgare
318862 149038286 Glycine max
245762 138329514 Bos taurus
242850 137255686 Xenopus laevis
182744 137143055 Medicago truncatula
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
3. FILE FORMATS
The flat file examples included in this section, while not always from the
current release, are usually fairly recent. Any differences compared to the
actual records are the result of updates to the entries involved.
3.1 File Header Information
With the exception of the index files, each of the 449 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) 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 2002
NCBI-GenBank Flat File Release 133.0
Bacterial Sequences (Part 1)
37811 loci, 97585608 bases, from 37811 reported sequences
---------+---------+---------+---------+---------+---------+---------+---------
1 10 20 30 40 50 60 70 79
Example 1. Sample File Header
3.2 Directory Files
3.2.1 Short Directory File
The short directory file contains brief descriptions of all of the
sequence entries contained in this release. These descriptions are in
fifteen groups, one group for each of the fifteen sequence entry
data files. The first record at the beginning of a group of entries
contains the name of the group in uppercase characters, beginning in
position 21. The organism groups are PRIMATE, RODENT, OTHER MAMMAL,
OTHER VERTEBRATE, INVERTEBRATE, PLANT, BACTERIAL, STRUCTURAL RNA, VIRAL,
PHAGE, SYNTHETIC, UNANNOTATED, EXPRESSED SEQUENCE TAG, PATENT, or
SEQUENCE TAGGED SITE. The second record is blank.
Each record in the short directory contains the sequence entry name
(LOCUS) in the first 12 positions, followed by a brief definition of
the sequence beginning in column 13. The definition is truncated (at
the end of a word) to leave room at the right margin for at least one
space, the sequence length, and the letters `bp'. The length of the
sequence is printed right-justified to column 77, followed by the
letters `bp' in columns 78 and 79. The next-to-last record for a group
has `ZZZZZZZZZZ' in its first ten positions (where the entry name
would normally appear). The last record is a blank line. An example of
the short directory file format, showing the descriptions of the last
entries in the Other Vertebrate sequence data file and the first
entries of the Invertebrate sequence data file, is reproduced below:
1 10 20 30 40 50 60 70 79
---------+---------+---------+---------+---------+---------+---------+---------
ZEFWNT1G3 B.rerio wnt-1 gene (exon 3) for wnt-1 protein. 266bp
ZEFWNT1G4 B.rerio wnt-1 gene (exon 4) for wnt-1 protein. 647bp
ZEFZF54 Zebrafish homeotic gene ZF-54. 246bp
ZEFZFEN Zebrafish engrailed-like homeobox sequence. 327bp
ZZZZZZZZZZ
INVERTEBRATE
AAHAV33A Acanthocheilonema viteae pepsin-inhibitor-like-protein 1048bp
ACAAC01 Acanthamoeba castelani gene encoding actin I. 1571bp
ACAACTPH Acanthamoeba castellanii actophorin mRNA, complete cds. 671bp
ACAMHCA A.castellanii non-muscle myosin heavy chain gene, partial 5894bp
---------+---------+---------+---------+---------+---------+---------+---------
1 10 20 30 40 50 60 70 79
Example 2. Short Directory File
3.3 Index Files
There are six files containing indices to the entries in this release:
Accession number index file (Accession and Version)
Secondary accession number index file
Keyword phrase index file
Author name index file
Journal citation index file
Gene name index file
The index keys (accession numbers, keywords, authors, journals, and
gene symbols.) of an index are sorted alphabetically. All index keys
appear in uppercase characters even though they appear in mixed case
in the sequence entries. Following each index key, the identifiers of the
sequence entries containing that key are listed (LOCUS name,
division abbreviation, and primary accession number). The division
abbreviations are:
1. PRI - primate sequences
2. ROD - rodent sequences
3. MAM - other mammalian sequences
4. VRT - other vertebrate sequences
5. INV - invertebrate sequences
6. PLN - plant, fungal, and algal sequences
7. BCT - bacterial sequences
8. VRL - viral sequences
9. PHG - bacteriophage sequences
10. SYN - synthetic sequences
11. UNA - unannotated sequences
12. EST - EST sequences (expressed sequence tags)
13. PAT - patent sequences
14. STS - STS sequences (sequence tagged sites)
15. GSS - GSS sequences (genome survey sequences)
16. HTG - HTGS sequences (high throughput genomic sequences)
17. HTC - HTC sequences (high throughput cDNA sequences)
A line-oriented, TAB-delimited format is utilized for the gbaut.idx,
gbgen.idx, gbjou.idx, gbkey.idx, and gbsec.idx indexes. Each index
key is presented on its own line, and is followed by a
LOCUS/Division/Accession triplet for every record containing the key:
Indexed-Term
LOCUS-name1 Div-code1 Accession1
LOCUS-name2 Div-code2 Accession2
LOCUS-name3 Div-code3 Accession3
....
Here is an example of the format, in which TAB characters are displayed
as ^I, and carriage-returns/newlines as $ :
(H+,K+)-ATPASE BETA-SUBUNIT$
^IRATHKATPB^IROD^IM55655$
^IMUSATP4B1^IROD^IM64685$
^IMUSATP4B2^IROD^IM64686$
^IMUSATP4B3^IROD^IM64687$
^IMUSATP4B4^IROD^IM64688$
^IDOGATPASEB^IMAM^IM76486$
When viewed by a file browser such as 'less' or 'more' :
(H+,K+)-ATPASE BETA-SUBUNIT
RATHKATPB ROD M55655
MUSATP4B1 ROD M64685
MUSATP4B2 ROD M64686
MUSATP4B3 ROD M64687
MUSATP4B4 ROD M64688
DOGATPASEB MAM M76486
Note that the index keys can be distinguished from LOCUS/DIV/ACCESSION
by the fact that they do not start with a TAB character. So one can
extract just the terms via simple text-processing:
perl -ne 'print unless /^\s+/' < gbkey.idx > terms.gbkey
The format of the primary accession number index file is slightly
different, with each indexed key (Accession.Version) present on
the same line as the LOCUS/Division/Accession triplet:
Accession1.Version1 Locus-name1 Div-code1 Accession1
Accession2.Version2 Locus-name2 Div-code2 Accession2
....
Here is an example of the format, in which TAB characters are displayed
as ^I, and carriage-returns/newlines as $ :
AC000102.1^IAC000102^IPRI^IAC000102$
AC000103.1^IAC000103^IPLN^IAC000103$
AC000104.1^IF19P19^IPLN^IAC000104$
AC000105.40^IAC000105^IPRI^IAC000105$
AC000106.1^IF7G19^IPLN^IAC000106$
AC000107.1^IAC000107^IPLN^IAC000107$
AC000108.1^IAC000108^IBCT^IAC000108$
AC000109.1^IHSAC000109^IPRI^IAC000109$
AC000110.1^IHSAC000110^IPRI^IAC000110$
When viewed by a file browser such as 'less' or 'more' :
AC000102.1 AC000102 PRI AC000102
AC000103.1 AC000103 PLN AC000103
AC000104.1 F19P19 PLN AC000104
AC000105.40 AC000105 PRI AC000105
AC000106.1 F7G19 PLN AC000106
AC000107.1 AC000107 PLN AC000107
AC000108.1 AC000108 BCT AC000108
AC000109.1 HSAC000109 PRI AC000109
AC000110.1 HSAC000110 PRI AC000110
3.3.1 Accession Number Index File - gbacc.idx
Accession numbers are unique six character or eight-character alphanumeric
identifiers of GenBank database entries. The six-character accession
number format consists of a single uppercase letter, followed by 5 digits.
The eight-character accession number format consists of two uppercase
letters, followed by 6 digits. Accessions provide an unchanging identifier
for the data with which they are associated, and we encourage you to cite
accession numbers whenever you refer to data from GenBank.
GenBank entries can have both 'primary' and 'secondary' accessions
associated with them (see Section 3.5.6). Only primary accessions are present
in the gbacc.idx index.
3.3.2 Keyword Phrase Index File - gbkey.idx
Keyword phrases consist of names for gene products and other
characteristics of sequence entries.
3.3.3 Author Name Index File - gbaut*.idx
The author name index files list all of the author names that appear
in the references within sequence records.
3.3.4 Journal Citation Index File - gbjou.idx
The journal citation index file lists all of the citations that appear
in the references within sequence records.. All citations are truncated
to 80 characters.
3.3.5 Gene Name Index - gbgen.idx
The /gene qualifiers of many GenBank entries contain values other than
official gene symbols, such as the product or the standard name of the gene.
Hence, NCBI has chosen to build an index (gbgen.idx) more like a keyword index
for this field, using both the GenBank /gene qualifier and the 'Gene.locus'
fields from the NCBI internal database as keys.
3.4 Sequence Entry Files
GenBank releases contain one or more sequence entry data files, one
for each "division" of GenBank.
3.4.1 File Organization
Each of these files has the same format and consists of two parts:
header information (described in section 3.1) and sequence entries for
that division (described in the following sections).
3.4.2 Entry Organization
In the second portion of a sequence entry file (containing the
sequence entries for that division), each record (line) consists of
two parts. The first part is found in positions 1 to 10 and may
contain:
1. A keyword, beginning in column 1 of the record (e.g., REFERENCE is
a keyword).
2. A subkeyword beginning in column 3, with columns 1 and 2 blank
(e.g., AUTHORS is a subkeyword of REFERENCE). Or a subkeyword beginning
in column 4, with columns 1, 2, and 3 blank (e.g., PUBMED is a
subkeyword of REFERENCE).
3. Blank characters, indicating that this record is a continuation of
the information under the keyword or subkeyword above it.
4. A code, beginning in column 6, indicating the nature of an entry
(feature key) in the FEATURES table; these codes are described in
Section 3.4.12.1 below.
5. A number, ending in column 9 of the record. This number occurs in
the portion of the entry describing the actual nucleotide sequence and
designates the numbering of sequence positions.
6. Two slashes (//) in positions 1 and 2, marking the end of an entry.
The second part of each sequence entry record contains the information
appropriate to its keyword, in positions 13 to 80 for keywords and
positions 11 to 80 for the sequence.
The following is a brief description of each entry field. Detailed
information about each field may be found in Sections 3.4.4 to 3.4.14.
LOCUS - A short mnemonic name for the entry, chosen to suggest the
sequence's definition. Mandatory keyword/exactly one record.
DEFINITION - A concise description of the sequence. Mandatory
keyword/one or more records.
ACCESSION - The primary accession number is a unique, unchanging
code assigned to each entry. (Please use this code when citing
information from GenBank.) Mandatory keyword/one or more records.
VERSION - A compound identifier consisting of the primary
accession number and a numeric version number associated with the
current version of the sequence data in the record. This is followed
by an integer key (a "GI") assigned to the sequence by NCBI.
Mandatory keyword/exactly one record.
NID - An alternative method of presenting the NCBI GI
identifier (described above). The NID is obsolete and was removed
from the GenBank flatfile format in December 1999.
KEYWORDS - Short phrases describing gene products and other
information about an entry. Mandatory keyword in all annotated
entries/one or more records.
SEGMENT - Information on the order in which this entry appears in a
series of discontinuous sequences from the same molecule. Optional
keyword (only in segmented entries)/exactly one record.
SOURCE - Common name of the organism or the name most frequently used
in the literature. Mandatory keyword in all annotated entries/one or
more records/includes one subkeyword.
ORGANISM - Formal scientific name of the organism (first line)
and taxonomic classification levels (second and subsequent lines).
Mandatory subkeyword in all annotated entries/two or more records.
REFERENCE - Citations for all articles containing data reported
in this entry. Includes seven subkeywords and may repeat. Mandatory
keyword/one or more records.
AUTHORS - Lists the authors of the citation. Optional
subkeyword/one or more records.
CONSRTM - Lists the collective names of consortiums associated
with the citation (eg, International Human Genome Sequencing Consortium),
rather than individual author names. Optional subkeyword/one or more records.
TITLE - Full title of citation. Optional subkeyword (present
in all but unpublished citations)/one or more records.
JOURNAL - Lists the journal name, volume, year, and page
numbers of the citation. Mandatory subkeyword/one or more records.
MEDLINE - Provides the Medline unique identifier for a
citation. Optional subkeyword/one record.
PUBMED - Provides the PubMed unique identifier for a
citation. Optional subkeyword/one record.
REMARK - Specifies the relevance of a citation to an
entry. Optional subkeyword/one or more records.
COMMENT - Cross-references to other sequence entries, comparisons to
other collections, notes of changes in LOCUS names, and other remarks.
Optional keyword/one or more records/may include blank records.
FEATURES - Table containing information on portions of the
sequence that code for proteins and RNA molecules and information on
experimentally determined sites of biological significance. Optional
keyword/one or more records.
BASE COUNT - Summary of the number of occurrences of each base
code in the sequence. Mandatory keyword/exactly one record.
ORIGIN - Specification of how the first base of the reported sequence
is operationally located within the genome. Where possible, this
includes its location within a larger genetic map. Mandatory
keyword/exactly one record.
- The ORIGIN line is followed by sequence data (multiple records).
// - Entry termination symbol. Mandatory at the end of an
entry/exactly one record.
3.4.3 Sample Sequence Data File
An example of a complete sequence entry file follows. (This example
has only two entries.) Note that in this example, as throughout the
data bank, numbers in square brackets indicate items in the REFERENCE
list. For example, in ACARR58S, [1] refers to the paper by Mackay, et
al.
1 10 20 30 40 50 60 70 79
---------+---------+---------+---------+---------+---------+---------+---------
GBSMP.SEQ Genetic Sequence Data Bank
15 December 1992
GenBank Flat File Release 74.0
Structural RNA Sequences
2 loci, 236 bases, from 2 reported sequences
LOCUS AAURRA 118 bp ss-rRNA RNA 16-JUN-1986
DEFINITION A.auricula-judae (mushroom) 5S ribosomal RNA.
ACCESSION K03160
VERSION K03160.1 GI:173593
KEYWORDS 5S ribosomal RNA; ribosomal RNA.
SOURCE A.auricula-judae (mushroom) ribosomal RNA.
ORGANISM Auricularia auricula-judae
Eukaryota; Fungi; Eumycota; Basidiomycotina; Phragmobasidiomycetes;
Heterobasidiomycetidae; Auriculariales; Auriculariaceae.
REFERENCE 1 (bases 1 to 118)
AUTHORS Huysmans,E., Dams,E., Vandenberghe,A. and De Wachter,R.
TITLE The nucleotide sequences of the 5S rRNAs of four mushrooms and
their use in studying the phylogenetic position of basidiomycetes
among the eukaryotes
JOURNAL Nucleic Acids Res. 11, 2871-2880 (1983)
FEATURES Location/Qualifiers
rRNA 1..118
/note="5S ribosomal RNA"
BASE COUNT 27 a 34 c 34 g 23 t
ORIGIN 5' end of mature rRNA.
1 atccacggcc ataggactct gaaagcactg catcccgtcc gatctgcaaa gttaaccaga
61 gtaccgccca gttagtacca cggtggggga ccacgcggga atcctgggtg ctgtggtt
//
LOCUS ABCRRAA 118 bp ss-rRNA RNA 15-SEP-1990
DEFINITION Acetobacter sp. (strain MB 58) 5S ribosomal RNA, complete sequence.
ACCESSION M34766
VERSION M34766.1 GI:173603
KEYWORDS 5S ribosomal RNA.
SOURCE Acetobacter sp. (strain MB 58) rRNA.
ORGANISM Acetobacter sp.
Prokaryotae; Gracilicutes; Scotobacteria; Aerobic rods and cocci;
Azotobacteraceae.
REFERENCE 1 (bases 1 to 118)
AUTHORS Bulygina,E.S., Galchenko,V.F., Govorukhina,N.I., Netrusov,A.I.,
Nikitin,D.I., Trotsenko,Y.A. and Chumakov,K.M.
TITLE Taxonomic studies of methylotrophic bacteria by 5S ribosomal RNA
sequencing
JOURNAL J. Gen. Microbiol. 136, 441-446 (1990)
FEATURES Location/Qualifiers
rRNA 1..118
/note="5S ribosomal RNA"
BASE COUNT 27 a 40 c 32 g 17 t 2 others
ORIGIN
1 gatctggtgg ccatggcggg agcaaatcag ccgatcccat cccgaactcg gccgtcaaat
61 gccccagcgc ccatgatact ctgcctcaag gcacggaaaa gtcggtcgcc gccagayy
//
---------+---------+---------+---------+---------+---------+---------+---------
1 10 20 30 40 50 60 70 79
Example 9. Sample Sequence Data File
3.4.4 LOCUS Format
The items of information contained in the LOCUS record are always
found in fixed positions. The locus name (or entry name), which is
always sixteen characters or less, begins in position 13. The locus name
is designed to help group entries with similar sequences: the first
three characters usually designate the organism; the fourth and fifth
characters can be used to show other group designations, such as gene
product; for segmented entries the last character is one of a series
of sequential integers.
The number of bases or base pairs in the sequence ends in position 40.
The letters `bp' are in positions 42 to 43. Positions 45 to 47 provide
the number of strands of the sequence. Positions 48 to 53 indicate the
type of molecule sequenced. Topology of the molecule is indicated in
positions 56 to 63.
GenBank sequence entries are divided among many different
'divisions'. Each entry's division is specified by a three-letter code
in positions 65 to 67. See Section 3.3 for an explanation of division
codes.
Positions 69 to 79 of the record contain the date the entry was
entered or underwent any substantial revisions, such as the addition
of newly published data, in the form dd-MMM-yyyy.
The detailed format for the LOCUS line format is as follows:
Positions Contents
--------- --------
01-05 'LOCUS'
06-12 spaces
13-28 Locus name
29-29 space
30-40 Length of sequence, right-justified
41-41 space
42-43 bp
44-44 space
45-47 spaces, ss- (single-stranded), ds- (double-stranded), or
ms- (mixed-stranded)
48-53 NA, DNA, RNA, tRNA (transfer RNA), rRNA (ribosomal RNA),
mRNA (messenger RNA), uRNA (small nuclear RNA), snRNA,
snoRNA. Left justified.
54-55 space
56-63 'linear' followed by two spaces, or 'circular'
64-64 space
65-67 The division code (see Section 3.3)
68-68 space
69-79 Date, in the form dd-MMM-yyyy (e.g., 15-MAR-1991)
Although each of these data values can be found at column-specific
positions, we encourage those who parse the contents of the LOCUS
line to use a token-based approach. This will prevent the need for
software changes if the spacing of the data values ever has to be
modified.
3.4.5 DEFINITION Format
The DEFINITION record gives a brief description of the sequence,
proceeding from general to specific. It starts with the common name of
the source organism, then gives the criteria by which this sequence is
distinguished from the remainder of the source genome, such as the
gene name and what it codes for, or the protein name and mRNA, or some
description of the sequence's function (if the sequence is
non-coding). If the sequence has a coding region, the description may
be followed by a completeness qualifier, such as cds (complete coding
sequence). There is no limit on the number of lines that may be part
of the DEFINITION. The last line must end with a period.
3.4.5.1 DEFINITION Format for NLM Entries
The DEFINITION line for entries derived from journal-scanning at the NLM is
an automatically generated descriptive summary that accompanies each DNA and
protein sequence. It contains information derived from fields in a database
that summarize the most important attributes of the sequence. The DEFINITION
lines are designed to supplement the accession number and the sequence itself
as a means of uniquely and completely specifying DNA and protein sequences. The
following are examples of NLM DEFINITION lines:
NADP-specific isocitrate dehydrogenase [swine, mRNA, 1 gene, 1585 nt]
94 kda fiber cell beaded-filament structural protein [rats, lens, mRNA
Partial, 1 gene, 1873 nt]
inhibin alpha {promoter and exons} [mice, Genomic, 1 gene, 1102 nt, segment
1 of 2]
cefEF, cefG=acetyl coenzyme A:deacetylcephalosporin C o-acetyltransferase
[Acremonium chrysogenum, Genomic, 2 genes, 2639 nt]
myogenic factor 3, qmf3=helix-loop-helix protein [Japanese quails,
embryo, Peptide Partial, 246 aa]
The first part of the definition line contains information describing
the genes and proteins represented by the molecular sequences. This can
be gene locus names, protein names and descriptions that replace or augment
actual names. Gene and gene product are linked by "=". Any special
identifying terms are presented within brackets, such as: {promoter},
{N-terminal}, {EC 2.13.2.4}, {alternatively spliced}, or {3' region}.
The second part of the definition line is delimited by square brackets, '[]',
and provides details about the molecule type and length. The biological
source, i.e., genus and species or common name as cited by the author.
Developmental stage, tissue type and strain are included if available.
The molecule types include: Genomic, mRNA, Peptide. and Other Genomic
Material. Genomic molecules are assumed to be partial sequence unless
"Complete" is specified, whereas mRNA and peptide molecules are assumed
to be complete unless "Partial" is noted.
3.4.6 ACCESSION Format
This field contains a series of six-character and/or eight-character
identifiers called 'accession numbers'. The six-character accession
number format consists of a single uppercase letter, followed by 5 digits.
The eight-character accession number format consists of two uppercase
letters, followed by 6 digits. The 'primary', or first, of the accession
numbers occupies positions 13 to 18 (6-character format) or positions
13 to 20 (8-character format). Subsequent 'secondary' accession numbers
(if present) are separated from the primary, and from each other, by a
single space. In some cases, multiple lines of secondary accession
numbers might be present, starting at position 13.
The primary accession number of a GenBank entry provides a stable identifier
for the biological object that the entry represents. Accessions do not change
when the underlying sequence data or associated features change.
Secondary accession numbers arise for a number of reasons. For example, a
single accession number may initially be assigned to a sequence described in
a publication. If it is later discovered that the sequence must be entered
into the database as multiple entries, each entry would receive a new primary
accession number, and the original accession number would appear as a secondary
accession number on each of the new entries.
3.4.7 VERSION Format
This line contains two types of identifiers for a GenBank database entry:
a compound accession number and an NCBI GI identifier.
LOCUS AF181452 1294 bp DNA PLN 12-OCT-1999
DEFINITION Hordeum vulgare dehydrin (Dhn2) gene, complete cds.
ACCESSION AF181452
VERSION AF181452.1 GI:6017929
^^^^^^^^^^ ^^^^^^^^^^
Compound NCBI GI
Accession Identifier
Number
A compound accession number consists of two parts: a stable, unchanging
primary-accession number portion (see Section 3.4.6 for a description of
accession numbers), and a sequentially increasing numeric version number.
The accession and version numbers are separated by a period. The initial
version number assigned to a new sequence is one. Compound accessions are
often referred to as "Accession.Version" .
An accession number allows one to retrieve the same biological object in the
database, regardless of any changes that are made to the entry over time. But
those changes can include changes to the sequence data itself, which is of
fundamental importance to many database users. So a numeric version number is
associated with the sequence data in every database entry. If an entry (for
example, AF181452) undergoes two sequence changes, its compound accession
number on the VERSION line would start as AF181452.1 . After the first sequence
change this would become: AF181452.2 . And after the second change: AF181452.3 .
The NCBI GI identifier of the VERSION line also serves as a method for
identifying the sequence data that has existed for a database entry over
time. GI identifiers are numeric values of one or more digits. Since they
are integer keys, they are less human-friendly than the Accession.Version
system described above. Returning to our example for AF181452, it was
initially assigned GI 6017929. If the sequence changes, a new integer GI will
be assigned, perhaps 7345003 . And after the second sequence change, perhaps
the GI would become 10456892 .
Why are both these methods for identifying the version of the sequence
associated with a database entry in use? For two reasons:
- Some data sources processed by NCBI for incorporation into its Entrez
sequence retrieval system do not version their own sequences.
- GIs provide a uniform, integer identifier system for every sequence
NCBI has processed. Some products and systems derived from (or reliant
upon) NCBI products and services prefer to use these integer identifiers
because they can all be processed in the same manner.
GenBank Releases contain only the most recent versions of all sequences
in the database. However, older versions can be obtained via GI-based or
Accession.Version-based queries with NCBI's web-Entrez and network-Entrez
applications. A sequence revision history web page is also available:
http://www.ncbi.nlm.nih.gov/htbin-post/Entrez/girevhist
NOTE: All the version numbers for the compound Accession.Version identifier
system were initialized to a value of one in February 1999, when that
system was introduced.
3.4.8 KEYWORDS Format
The KEYWORDS field does not appear in unannotated entries, but is
required in all annotated entries. Keywords are separated by
semicolons; a "keyword" may be a single word or a phrase consisting of
several words. Each line in the keywords field ends in a semicolon;
the last line ends with a period. If no keywords are included in the
entry, the KEYWORDS record contains only a period.
3.4.9 SEGMENT Format
The SEGMENT keyword is used when two (or more) entries of known
relative orientation are separated by a short (<10 kb) stretch of DNA.
It is limited to one line of the form `n of m', where `n' is the
segment number of the current entry and `m' is the total number of
segments.
3.4.10 SOURCE Format
The SOURCE field consists of two parts. The first part is found after
the SOURCE keyword and contains free-format information including an
abbreviated form of the organism name followed by a molecule type;
multiple lines are allowed, but the last line must end with a period.
The second part consists of information found after the ORGANISM
subkeyword. The formal scientific name for the source organism (genus
and species, where appropriate) is found on the same line as ORGANISM.
The records following the ORGANISM line list the taxonomic
classification levels, separated by semicolons and ending with a
period.
3.4.11 REFERENCE Format
The REFERENCE field consists of five parts: the keyword REFERENCE, and
the subkeywords AUTHORS, TITLE (optional), JOURNAL, MEDLINE (optional),
PUBMED (optional), and REMARK (optional).
The REFERENCE line contains the number of the particular reference and
(in parentheses) the range of bases in the sequence entry reported in
this citation. Additional prose notes may also be found within the
parentheses. The numbering of the references does not reflect
publication dates or priorities.
The AUTHORS line lists the authors in the order in which they appear
in the cited article. Last names are separated from initials by a
comma (no space); there is no comma before the final `and'. The list
of authors ends with a period. The TITLE line is an optional field,
although it appears in the majority of entries. It does not appear in
unpublished sequence data entries that have been deposited directly
into the GenBank data bank, the EMBL Nucleotide Sequence Data Library,
or the DNA Data Bank of Japan. The TITLE field does not end with a
period.
The JOURNAL line gives the appropriate literature citation for the
sequence in the entry. The word `Unpublished' will appear after the
JOURNAL subkeyword if the data did not appear in the scientific
literature, but was directly deposited into the data bank. For
published sequences the JOURNAL line gives the Thesis, Journal, or
Book citation, including the year of publication, the specific
citation, or In press.
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 133.0) 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
Nancy Allmang, Medha Bhagwat, Peter Cooper, Susan Dombrowski,
Renata Geer, Dawn Lipshultz, Eugenia Posey-Marcos, Scott McGinnis,
Vyvy Pham, Barbara Rapp, Monica Romiti, Tao Tao, Rose Marie Woodsmall,
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
