Release Notes For GenBank Release 136
GBREL.TXT Genetic Sequence Data Bank
June 15 2003
NCBI-GenBank Flat File Release 136.0
Distribution Release Notes
25592865 loci, 32528249295 bases, from 25592865 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 136.0
1.2 Cutoff Date
1.3 Important Changes in Release 136.0
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 136.0
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 136.0 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, 136.0, incorporates data available to the collaborating
databases as of June 12, 2003. For more recent data, users are advised to:
o Download the GenBank Update files by anonymous FTP to 'ftp.ncbi.nih.gov':
ftp://ftp.ncbi.nih.gov/ncbi-asn1 (ASN.1 format)
ftp://ftp.ncbi.nih.gov/genbank (flatfile format)
Mirrors of the GenBank FTP site at the NCBI are available from the San Diego
Supercomputer Center and the University of Indiana:
ftp://genbank.sdsc.edu/pub
ftp://bio-mirror.net/biomirror/genbank/
Some users who experience slow FTP transfers of large files (entire releases,
the GenBank Cumulative Update, etc) might realize an improvement in transfer
rates from these alternate sites when traffic at the NCBI is high.
o Use the interactive Network-Entrez or Web-Entrez applications to query
the 'Entrez: Nucleotides' database (see Section 6.4 of this document).
1.3 Important Changes in Release 136.0
1.3.1 Organizational changes
The total number of sequence data files increased by 26 with this release:
- the EST division is now comprised of 259 files (+15)
- the GSS division is now comprised of 77 files (+7)
- the PLN division is now comprised of 8 files (+1)
- the ROD division is now comprised of 8 files (+1)
- the STS division is now comprised of 3 files (+1)
- the VRT division is now comprised of 3 files (+1)
1.3.2 Erratum : Release 135.0 release notes (April 2003)
The description of the /locus_tag qualifier in the GenBank 135.0
release notes erroneously states that it is intended for use on
the source feature. In fact, /locus_tag is used for gene, coding
region, and other features, and is not utilized by the source
feature. See the Feature Table documentation for complete details
regarding qualifier usage:
http://www.ncbi.nlm.nih.gov/projects/collab/FT/index.html
In addition, we noticed that the release notes for GenBank 133.0
(December, 2002) and GenBank 134.0 (February 2003) referred to the
upcoming April 2003 release as number 134.0 rather than 135.0 .
Our apologies for any confusion that these errors may have caused,
especially regarding the timeline for introduction of /locus_tag,
/mol_type, and /segment .
1.3.3 GSS File Header Problem
GSS sequences at GenBank are maintained in one of two different systems,
depending on their origin. One recent change to release processing involves
the parallelization of the dumps from those systems. Because the second dump
(for example) has no prior knowledge of exactly how many GSS files will be
dumped from the first, it doesn't know how to number it's own output files.
There is thus a discrepancy between the filenames and file headers of eleven
GSS flatfiles in Release 136.0. Consider the gbgss67.seq file:
GBGSS1.SEQ Genetic Sequence Data Bank
June 15 2003
NCBI-GenBank Flat File Release 136.0
GSS Sequences (Part 1)
86693 loci, 65544901 bases, from 86693 reported sequences
Here, the filename and part number in the header is "1", though the file
has been renamed as "67" 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 Sequence Length Limitation To Be Removed In June 2004
At the May 2003 collaborative meeting among representatives of GenBank,
EMBL, and DDBJ, it was decided that the 350 kilobase limit on the sequence
length of database records will be removed as of June 2004.
Individual, complete sequences are currently expected to be a maximum
of 350 kbp in length. One major reason for the existence of this limit is
as an aid to users of sequence analysis software, some of which might not
be capable of processing megabase-scale sequences.
However, very significant exceptions to the 350 kbp limit have existed
for several years; Phase 1 (unordered, unoriented) and Phase 2 (ordered,
oriented) high-throughput genomic sequences (HTGS) generated by efforts
such as the Human Genome Project; large dispersed eukaryotic genes with
an intron/exon structure that spans more than 350 kbp; and sequences
which result from assemblies of Whole Genome Shotgun (WGS) project data.
Given these exceptions, and the technological advances which have made
large-scale sequencing practical for an increasing number of researchers,
the collaboration has decided that the 350 kbp limit must be removed.
As of June 2004, the length of database sequences will be limited only
by the natural structures of an organism's genome. For example, a single
record might be used to represent all of human chromosome 1, which is
approximately 245 Mbp in length.
Software developers for some of the larger commercial sequence analysis
packages were recently asked what timeframe would be appropriate for this
change. Answers ranged from "immediately", to "several months", to "one year".
So
which result from assemblies of Whole Genome Shotgun (WGS) project data.
Given these exceptions, and the technological advances which have made
large-scale sequencing practical for an increasing number of researchers,
the collaboration has decided that the 350 kbp limit must be removed.
As of June 2004, the length of database sequences will be limited only
by the natural structures of an organism's genome. For example, a single
record might be used to represent all of human chromosome 1, which is
approximately 245 Mbp in length.
Software developers for some of the larger commercial sequence analysis
packages were recently asked what timeframe would be appropriate for this
change. Answers ranged from "immediately", to "several months", to "one year".
So
which result from assemblies of Whole Genome Shotgun (WGS) project data.
Given these exceptions, and the technological advances which have made
large-scale sequencing practical for an increasing number of researchers,
the collaboration has decided that the 350 kbp limit must be removed.
As of June 2004, the length of database sequences will be limited only
by the natural structures of an organism's genome. For example, a single
record might be used to represent all of human chromosome 1, which is
approximately 245 Mbp in length.
Software developers for some of the larger commercial sequence analysis
packages were recently asked what timeframe would be appropriate for this
change. Answers ranged from "immediately", to "several months", to "one year".
So the one-year timeframe was selected, to provide ample time to implement
changes which megabase-scale sequences may require.
Some sample records with very large sequences have been made available
so that developers can begin to test their software modifications:
ftp://ftp.ncbi.nih.gov/genbank/LargeSeqs
Many changes are expected after the removal of the length limit. For
example, complete bacterial genomes (typically on the order of several
megabases) will be re-assembled into single sequence records. The submission
process for such genomes will become much more streamlined, since database
staff will no longer have to split the genomes into pieces. BLAST services
will be enchanced, so that hits reported within very large sequences will
be presented in a meaningful context.
All such changes will be discussed more fully in future release notes,
the NCBI newsletter, and the GenBank newsgroup.
1.4.2 BASECOUNT line to be dropped
The BASECOUNT line of the GenBank flatfile format provides totals for
the number of A, T, G, C, and 'other' basepairs that are present within
the sequence of a database record. For example:
LOCUS AY244763 5686 bp DNA linear BCT 10-APR-2003
DEFINITION Rhodococcus sp. DS7 cysDNCQ operon, complete sequence.
ACCESSION AY244763
VERSION AY244763.1 GI:29725657
....
BASE COUNT 1137 a 1661 c 1821 g 1066 t 1 others
ORIGIN
1 cgcggtttgt gacgtctgat tgccggtcat tgacctttgg gtagaacgag ttctattctg
61 tgattgcgtt caatttagaa ccagtccggt acataaatgt accgatgcgg aaatggtgtt
....
5281 tgtcagctcg gtgtctggng gcgaggctaa gcaccaacgg cttcggtagc agaaccacat
This information is computationally expensive to produce for very large
sequences, and for sequences in the CON division. In the CON division case,
a record might be comprised of 'pointers' to hundreds, or even thousands,
of underlying GenBank records. So to calculate the BASECOUNT line content,
retrievals of sequence data for those many records must be performed. This
can noticeably impact the response time for flatfile generation within the
Entrez application.
Hence, as of the October 2003 GenBank Release (138.0), the BASECOUNT linetype
will no longer be present in GenBank Release and GenBank Update products.
Depending on demand, a display option might be implemented in Entrez which
allows users to choose to have BASECOUNT shown.
1.4.3 New oriT feature
As of Release 138.0 in October 2003, a new feature key (oriT) will be
legal for the feature table. Preliminary documentation for this new
feature is available:
Feature Key oriT
Definition origin of transfer; region of a plasmid where
transfer is initiated during the process of
conjugation or mobilisation.
Mandatory qualifiers: None
Optional Qualifiers: /bound_moiety="text"
/citation=[number]
/db_xref="<database>:<identifier>"
/direction=value
/evidence=<evidence_value>
/gene="text"
/label=feature_label
/locus_tag="text" (single token)
/map="text"
/note="text"
/rpt_family="text"
/rpt_type=<repeat_type>
/rpt_unit=<feature_label>
/standard_name="text"
/usedin=accnum:feature_label
Molecule Scope: DNA
Comments: rep_origin should be used for origins
of replication; /direction has
legal values RIGHT, LEFT and BOTH,
however only RIGHT and LEFT are valid
when used in conjunction with the oriT
feature
1.4.4 New /ecotype qualifier
As of the October 2003 GenBank Release (138.0), a new source feature
qualifier called /ecotype will begin to be used. The preliminary
definition for /ecotype is :
Qualifier /ecotype=
Definition A distinct population of organisms of a
widespread species that has adapted
gentically to its own local habitat.
Nevertheless, they can still reproduce
with members of other ecotypes of the
same species.
Value format "text"
Example /ecotype="Columbia"
Comment 'Ecotype' is often applied to standard
genetic stocks of Arabidopsis thaliana,
but it can be applied to any organism,
especially sessile organisms like plants.
1.4.5 Change to value format of /rpt_unit
As of Release 138.0 in October 2003, the value-format of the /rpt_unit
qualifier will be changed to allow 'text' . The currently documented
format is:
Value format <feature_label> or <base_range>
Example /rpt_unit=Alu_rpt1
/rpt_unit=202..245
Comment used to indicate feature which defines (or base range of) the
repeat unit of which a repeat region is made
However, a very common value for /rpt_unit is a literal sequence
string that represents the repeating unit(s). For example:
/rpt_unit=ta
/rpt_unit=ac;ag
So the format of this qualifier will be changed to:
Value format "text" or <feature_label> or <base_range>
Existing feature label and base range values will eventually presented
as text values.
1.4.6 New operon feature
Starting with the October 2003 release (138.0), a new feature will be
legal for the feature table:
Feature Key: operon
Definition: region containing polycistronic transcripts
and regulatory sequences containing genes
that encode enzymes that are in the same
metabolic pathway
Optional qualifiers: /allele="text"
/citation=[number]
/db_xref="<database>:<identifier>"
/evidence=<evidence_value>
/function="text"
/operon="text"
/label=feature_label
/locus_tag="text" (single token)
/map="text"
/note="text"
/product="text"
/pseudo
/phenotype="text"
/standard_name="text"
/usedin=accnum:feature_label
In bacteria, many genes encoding for specific biosynthetic pathways are
transcribed in polycistronic operons. It has been challenging to reflect
this biology within the GenBank flatfile format. GenBank has been using
a gene feature that spans the entire regulatory region and all of the coding
regions and then gene features corresponding to the individual genes spaning
the coding genes.
The new operon feature will simplify the annotation of cases like
these. Examples of the new operon feature will be provided in future
release notes.
1.4.7 [er] prefix for JOURNAL line
As of Release 138.0 in October 2003, a new prefix will be legal for the
JOURNAL line: [er] .
This prefix is an abbreviation for Electronic Resource, which is a
term that describes journal articles that are available on-line.
In 1999, an interim 'Online Publication' REFERENCE format was adopted for
use at GenBank in order to cite articles appearing only electronically:
REFERENCE 1 (bases 1 to 2858)
AUTHORS Smith, J.
TITLE Cloning and expression of a phospholipase gene
JOURNAL Online Publication
REMARK Online-Journal-name; Article Identifier; URL
In subsequent years, no standards for citing on-line journal articles
have emerged from library organizations.
One such library organization (National Library of Medicine, NIH) is now
assigning identifiers (Medline UIs and PubMed Ids) to articles published
on-line, and it is presenting these articles in a manner that is identical
to print-journal articles. For example:
REFERENCE 1
AUTHORS Haas,B.J., Volfovsky,N., Town,C.D., Troukhan,M., Alexandrov,N.,
Feldmann,K.A., Flavell,R.B., White,O. and Salzberg,S.L.
TITLE Full-length messenger RNA sequences greatly improve genome
annotation
JOURNAL Genome Biol. 3 (6), RESEARCH0029 (2002)
MEDLINE 22088475
PUBMED 12093376
Although these citations may contain journal abbreviations, volume numbers,
issue/part/supplement numbers, pages, and year (just like a print-journal
citation), there is no guarantee that the contents of these fields will be
comparable to those of print-journal citations.
In the case above, although the page number is a bit unusual
("RESEARCH0029"), software processing the JOURNAL line would probably still
be able to parse its contents. But there is also a possibility that these
fields could contain unusual characters (embedded spaces, commas, parentheses),
and possibly even URLs. So the addition of [er] :
JOURNAL [er] Genome Biol. 3 (6), RESEARCH0029 (2002)
will act as a warning (primarily to software) that the contents of the
JOURNAL line might not be as parsable as a print-journal JOURNAL line.
1.4.8 Accession format of WGS records
Whole Genome Shotgun (WGS) sequences utilize an accession number format which
is different from those used for non-WGS GenBank sequences. This format is
referred to as 4 + 2 + 6, and is comprised of:
- a 4-letter WGS project code
- a 2-digit assembly-version number
- a 6 (and sometimes 7) digit sequence number
Because of their unique nature, WGS sequences are kept separate from other
GenBank products:
ftp://ftp.ncbi.nih.gov/genbank/wgs
For example, sequences much larger than the current 350 kbp limit can be
generated during the WGS assembly phase. In addition, there is no tracking
of nucleotide sequences from one assembly to the next. So the accessions
of one:
AAAB01000001
AAAB01000002
AAAB01000003
....
are not necessarily related in any way to those of the next assembly:
AAAB02000001
AAAB02000002
AAAB02000003
....
When a WGS project is completed, it is possible that the submittors may chose
to submit a single finished WGS sequence with a 4 + 2 + 6 accession, at which
point it would appear in the non-WGS portion of GenBank.
Alternately, the submittors might chose to submit the completed genome via
a non-WGS method, in which case a de-novo non-WGS accession would be assigned.
That record would then have one or more 2 + 4 + 6 WGS accessions as
secondary accessions.
Both scenarios are likely to occur, especially after the 350 kbp sequence
length restriction is lifted. So we felt it was important to alert users
that WGS accessions will eventually be encountered in the non-WGS portion
of GenBank, as primary or secondary accession numbers.
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 508 files. The lists
that follow describe each of the files included in the distribution.
Their sizes and base pair content are also summarized.
2.2.1 File Descriptions
1. gbrel.txt - Release notes (this document).
2. gbsdr.txt - Short directory of the data bank.
3. gbacc.idx - Index of the entries according to accession number.
4. gbkey.idx - Index of the entries according to keyword phrase.
5. gbaut1.idx - Index of the entries according to author, part 1.
6. gbaut2.idx - Index of the entries according to author, part 2.
7. gbaut3.idx - Index of the entries according to author, part 3.
8. gbaut4.idx - Index of the entries according to author, part 4.
9. gbaut5.idx - Index of the entries according to author, part 5.
10. gbaut6.idx - Index of the entries according to author, part 6.
11. gbaut7.idx - Index of the entries according to author, part 7.
12. gbaut8.idx - Index of the entries according to author, part 8.
13. gbaut9.idx - Index of the entries according to author, part 9.
14. gbaut10.idx - Index of the entries according to author, part 10.
15. gbaut11.idx - Index of the entries according to author, part 11.
16. gbaut12.idx - Index of the entries according to author, part 12.
17. gbaut13.idx - Index of the entries according to author, part 13.
18. gbaut14.idx - Index of the entries according to author, part 14.
19. gbaut15.idx - Index of the entries according to author, part 15.
20. gbaut16.idx - Index of the entries according to author, part 16.
21. gbaut17.idx - Index of the entries according to author, part 17.
22. gbaut18.idx - Index of the entries according to author, part 18.
23. gbaut19.idx - Index of the entries according to author, part 19.
24. gbaut20.idx - Index of the entries according to author, part 20.
25. gbjou.idx - Index of the entries according to journal citation.
26. gbgen.idx - Index of the entries according to gene names.
27. gbsec.idx - Index of the entries according to secondary accession number.
28. gbpri1.seq - Primate sequence entries, part 1.
29. gbpri2.seq - Primate sequence entries, part 2.
30. gbpri3.seq - Primate sequence entries, part 3.
31. gbpri4.seq - Primate sequence entries, part 4.
32. gbpri5.seq - Primate sequence entries, part 5.
33. gbpri6.seq - Primate sequence entries, part 6.
34. gbpri7.seq - Primate sequence entries, part 7.
35. gbpri8.seq - Primate sequence entries, part 8.
36. gbpri9.seq - Primate sequence entries, part 9.
37. gbpri10.seq - Primate sequence entries, part 10.
38. gbpri11.seq - Primate sequence entries, part 11.
39. gbpri12.seq - Primate sequence entries, part 12.
40. gbpri13.seq - Primate sequence entries, part 13.
41. gbpri14.seq - Primate sequence entries, part 14.
42. gbpri15.seq - Primate sequence entries, part 15.
43. gbpri16.seq - Primate sequence entries, part 16.
44. gbpri17.seq - Primate sequence entries, part 17.
45. gbpri18.seq - Primate sequence entries, part 18.
46. gbpri19.seq - Primate sequence entries, part 19.
47. gbpri20.seq - Primate sequence entries, part 20.
48. gbpri21.seq - Primate sequence entries, part 21.
49. gbpri22.seq - Primate sequence entries, part 22.
50. gbpri23.seq - Primate sequence entries, part 23.
51. gbpri24.seq - Primate sequence entries, part 24.
52. gbpri25.seq - Primate sequence entries, part 25.
53. gbrod1.seq - Rodent sequence entries, part 1.
54. gbrod2.seq - Rodent sequence entries, part 2.
55. gbrod3.seq - Rodent sequence entries, part 3.
56. gbrod4.seq - Rodent sequence entries, part 4.
57. gbrod5.seq - Rodent sequence entries, part 5.
58. gbrod6.seq - Rodent sequence entries, part 6.
59. gbrod7.seq - Rodent sequence entries, part 7.
60. gbrod8.seq - Rodent sequence entries, part 8.
61. gbmam.seq - Other mammalian sequence entries.
62. gbvrt1.seq - Other vertebrate sequence entries, part 1.
63. gbvrt2.seq - Other vertebrate sequence entries, part 2.
64. gbvrt3.seq - Other vertebrate sequence entries, part 3.
65. gbinv1.seq - Invertebrate sequence entries, part 1.
66. gbinv2.seq - Invertebrate sequence entries, part 2.
67. gbinv3.seq - Invertebrate sequence entries, part 3.
68. gbinv4.seq - Invertebrate sequence entries, part 4.
69. gbinv5.seq - Invertebrate sequence entries, part 5.
70. gbinv6.seq - Invertebrate sequence entries, part 6.
71. gbpln1.seq - Plant sequence entries (including fungi and algae), part 1.
72. gbpln2.seq - Plant sequence entries (including fungi and algae), part 2.
73. gbpln3.seq - Plant sequence entries (including fungi and algae), part 3.
74. gbpln4.seq - Plant sequence entries (including fungi and algae), part 4.
75. gbpln5.seq - Plant sequence entries (including fungi and algae), part 5.
76. gbpln6.seq - Plant sequence entries (including fungi and algae), part 6.
77. gbpln7.seq - Plant sequence entries (including fungi and algae), part 7.
78. gbpln8.seq - Plant sequence entries (including fungi and algae), part 8.
79. gbbct1.seq - Bacterial sequence entries, part 1.
80. gbbct2.seq - Bacterial sequence entries, part 2.
81. gbbct3.seq - Bacterial sequence entries, part 3.
82. gbbct4.seq - Bacterial sequence entries, part 4.
83. gbbct5.seq - Bacterial sequence entries, part 5.
84. gbbct6.seq - Bacterial sequence entries, part 6.
85. gbbct7.seq - Bacterial sequence entries, part 7.
86. gbvrl1.seq - Viral sequence entries, part 1.
87. gbvrl2.seq - Viral sequence entries, part 2.
88. gbvrl3.seq - Viral sequence entries, part 3.
89. gbphg.seq - Phage sequence entries.
90. gbsyn.seq - Synthetic and chimeric sequence entries.
91. gbuna.seq - Unannotated sequence entries.
92. gbest1.seq - EST (expressed sequence tag) sequence entries, part 1.
93. gbest2.seq - EST (expressed sequence tag) sequence entries, part 2.
94. gbest3.seq - EST (expressed sequence tag) sequence entries, part 3.
95. gbest4.seq - EST (expressed sequence tag) sequence entries, part 4.
96. gbest5.seq - EST (expressed sequence tag) sequence entries, part 5.
97. gbest6.seq - EST (expressed sequence tag) sequence entries, part 6.
98. gbest7.seq - EST (expressed sequence tag) sequence entries, part 7.
99. gbest8.seq - EST (expressed sequence tag) sequence entries, part 8.
100. gbest9.seq - EST (expressed sequence tag) sequence entries, part 9.
101. gbest10.seq - EST (expressed sequence tag) sequence entries, part 10.
102. gbest11.seq - EST (expressed sequence tag) sequence entries, part 11.
103. gbest12.seq - EST (expressed sequence tag) sequence entries, part 12.
104. gbest13.seq - EST (expressed sequence tag) sequence entries, part 13.
105. gbest14.seq - EST (expressed sequence tag) sequence entries, part 14.
106. gbest15.seq - EST (expressed sequence tag) sequence entries, part 15.
107. gbest16.seq - EST (expressed sequence tag) sequence entries, part 16.
108. gbest17.seq - EST (expressed sequence tag) sequence entries, part 17.
109. gbest18.seq - EST (expressed sequence tag) sequence entries, part 18.
110. gbest19.seq - EST (expressed sequence tag) sequence entries, part 19.
111. gbest20.seq - EST (expressed sequence tag) sequence entries, part 20.
112. gbest21.seq - EST (expressed sequence tag) sequence entries, part 21.
113. gbest22.seq - EST (expressed sequence tag) sequence entries, part 22.
114. gbest23.seq - EST (expressed sequence tag) sequence entries, part 23.
115. gbest24.seq - EST (expressed sequence tag) sequence entries, part 24.
116. gbest25.seq - EST (expressed sequence tag) sequence entries, part 25.
117. gbest26.seq - EST (expressed sequence tag) sequence entries, part 26.
118. gbest27.seq - EST (expressed sequence tag) sequence entries, part 27.
119. gbest28.seq - EST (expressed sequence tag) sequence entries, part 28.
120. gbest29.seq - EST (expressed sequence tag) sequence entries, part 29.
121. gbest30.seq - EST (expressed sequence tag) sequence entries, part 30.
122. gbest31.seq - EST (expressed sequence tag) sequence entries, part 31.
123. gbest32.seq - EST (expressed sequence tag) sequence entries, part 32.
124. gbest33.seq - EST (expressed sequence tag) sequence entries, part 33.
125. gbest34.seq - EST (expressed sequence tag) sequence entries, part 34.
126. gbest35.seq - EST (expressed sequence tag) sequence entries, part 35.
127. gbest36.seq - EST (expressed sequence tag) sequence entries, part 36.
128. gbest37.seq - EST (expressed sequence tag) sequence entries, part 37.
129. gbest38.seq - EST (expressed sequence tag) sequence entries, part 38.
130. gbest39.seq - EST (expressed sequence tag) sequence entries, part 39.
131. gbest40.seq - EST (expressed sequence tag) sequence entries, part 40.
132. gbest41.seq - EST (expressed sequence tag) sequence entries, part 41.
133. gbest42.seq - EST (expressed sequence tag) sequence entries, part 42.
134. gbest43.seq - EST (expressed sequence tag) sequence entries, part 43.
135. gbest44.seq - EST (expressed sequence tag) sequence entries, part 44.
136. gbest45.seq - EST (expressed sequence tag) sequence entries, part 45.
137. gbest46.seq - EST (expressed sequence tag) sequence entries, part 46.
138. gbest47.seq - EST (expressed sequence tag) sequence entries, part 47.
139. gbest48.seq - EST (expressed sequence tag) sequence entries, part 48.
140. gbest49.seq - EST (expressed sequence tag) sequence entries, part 49.
141. gbest50.seq - EST (expressed sequence tag) sequence entries, part 50.
142. gbest51.seq - EST (expressed sequence tag) sequence entries, part 51.
143. gbest52.seq - EST (expressed sequence tag) sequence entries, part 52.
144. gbest53.seq - EST (expressed sequence tag) sequence entries, part 53.
145. gbest54.seq - EST (expressed sequence tag) sequence entries, part 54.
146. gbest55.seq - EST (expressed sequence tag) sequence entries, part 55.
147. gbest56.seq - EST (expressed sequence tag) sequence entries, part 56.
148. gbest57.seq - EST (expressed sequence tag) sequence entries, part 57.
149. gbest58.seq - EST (expressed sequence tag) sequence entries, part 58.
150. gbest59.seq - EST (expressed sequence tag) sequence entries, part 59.
151. gbest60.seq - EST (expressed sequence tag) sequence entries, part 60.
152. gbest61.seq - EST (expressed sequence tag) sequence entries, part 61.
153. gbest62.seq - EST (expressed sequence tag) sequence entries, part 62.
154. gbest63.seq - EST (expressed sequence tag) sequence entries, part 63.
155. gbest64.seq - EST (expressed sequence tag) sequence entries, part 64.
156. gbest65.seq - EST (expressed sequence tag) sequence entries, part 65.
157. gbest66.seq - EST (expressed sequence tag) sequence entries, part 66.
158. gbest67.seq - EST (expressed sequence tag) sequence entries, part 67.
159. gbest68.seq - EST (expressed sequence tag) sequence entries, part 68.
160. gbest69.seq - EST (expressed sequence tag) sequence entries, part 69.
161. gbest70.seq - EST (expressed sequence tag) sequence entries, part 70.
162. gbest71.seq - EST (expressed sequence tag) sequence entries, part 71.
163. gbest72.seq - EST (expressed sequence tag) sequence entries, part 72.
164. gbest73.seq - EST (expressed sequence tag) sequence entries, part 73.
165. gbest74.seq - EST (expressed sequence tag) sequence entries, part 74.
166. gbest75.seq - EST (expressed sequence tag) sequence entries, part 75.
167. gbest76.seq - EST (expressed sequence tag) sequence entries, part 76.
168. gbest77.seq - EST (expressed sequence tag) sequence entries, part 77.
169. gbest78.seq - EST (expressed sequence tag) sequence entries, part 78.
170. gbest79.seq - EST (expressed sequence tag) sequence entries, part 79.
171. gbest80.seq - EST (expressed sequence tag) sequence entries, part 80.
172. gbest81.seq - EST (expressed sequence tag) sequence entries, part 81.
173. gbest82.seq - EST (expressed sequence tag) sequence entries, part 82.
174. gbest83.seq - EST (expressed sequence tag) sequence entries, part 83.
175. gbest84.seq - EST (expressed sequence tag) sequence entries, part 84.
176. gbest85.seq - EST (expressed sequence tag) sequence entries, part 85.
177. gbest86.seq - EST (expressed sequence tag) sequence entries, part 86.
178. gbest87.seq - EST (expressed sequence tag) sequence entries, part 87.
179. gbest88.seq - EST (expressed sequence tag) sequence entries, part 88.
180. gbest89.seq - EST (expressed sequence tag) sequence entries, part 89
181. gbest90.seq - EST (expressed sequence tag) sequence entries, part 90.
182. gbest91.seq - EST (expressed sequence tag) sequence entries, part 91.
183. gbest92.seq - EST (expressed sequence tag) sequence entries, part 92.
184. gbest93.seq - EST (expressed sequence tag) sequence entries, part 93.
185. gbest94.seq - EST (expressed sequence tag) sequence entries, part 94.
186. gbest95.seq - EST (expressed sequence tag) sequence entries, part 95.
187. gbest96.seq - EST (expressed sequence tag) sequence entries, part 96.
188. gbest97.seq - EST (expressed sequence tag) sequence entries, part 97.
189. gbest98.seq - EST (expressed sequence tag) sequence entries, part 98.
190. gbest99.seq - EST (expressed sequence tag) sequence entries, part 99.
191. gbest100.seq - EST (expressed sequence tag) sequence entries, part 100.
192. gbest101.seq - EST (expressed sequence tag) sequence entries, part 101.
193. gbest102.seq - EST (expressed sequence tag) sequence entries, part 102.
194. gbest103.seq - EST (expressed sequence tag) sequence entries, part 103.
195. gbest104.seq - EST (expressed sequence tag) sequence entries, part 104.
196. gbest105.seq - EST (expressed sequence tag) sequence entries, part 105.
197. gbest106.seq - EST (expressed sequence tag) sequence entries, part 106.
198. gbest107.seq - EST (expressed sequence tag) sequence entries, part 107.
199. gbest108.seq - EST (expressed sequence tag) sequence entries, part 108.
200. gbest109.seq - EST (expressed sequence tag) sequence entries, part 109.
201. gbest110.seq - EST (expressed sequence tag) sequence entries, part 110.
202. gbest111.seq - EST (expressed sequence tag) sequence entries, part 111.
203. gbest112.seq - EST (expressed sequence tag) sequence entries, part 112.
204. gbest113.seq - EST (expressed sequence tag) sequence entries, part 113.
205. gbest114.seq - EST (expressed sequence tag) sequence entries, part 114.
206. gbest115.seq - EST (expressed sequence tag) sequence entries, part 115.
207. gbest116.seq - EST (expressed sequence tag) sequence entries, part 116.
208. gbest117.seq - EST (expressed sequence tag) sequence entries, part 117.
209. gbest118.seq - EST (expressed sequence tag) sequence entries, part 118.
210. gbest119.seq - EST (expressed sequence tag) sequence entries, part 119.
211. gbest120.seq - EST (expressed sequence tag) sequence entries, part 120.
212. gbest121.seq - EST (expressed sequence tag) sequence entries, part 121.
213. gbest122.seq - EST (expressed sequence tag) sequence entries, part 122.
214. gbest123.seq - EST (expressed sequence tag) sequence entries, part 123.
215. gbest124.seq - EST (expressed sequence tag) sequence entries, part 124.
216. gbest125.seq - EST (expressed sequence tag) sequence entries, part 125.
217. gbest126.seq - EST (expressed sequence tag) sequence entries, part 126.
218. gbest127.seq - EST (expressed sequence tag) sequence entries, part 127.
219. gbest128.seq - EST (expressed sequence tag) sequence entries, part 128.
220. gbest129.seq - EST (expressed sequence tag) sequence entries, part 129.
221. gbest130.seq - EST (expressed sequence tag) sequence entries, part 130.
222. gbest131.seq - EST (expressed sequence tag) sequence entries, part 131.
223. gbest132.seq - EST (expressed sequence tag) sequence entries, part 132.
224. gbest133.seq - EST (expressed sequence tag) sequence entries, part 133.
225. gbest134.seq - EST (expressed sequence tag) sequence entries, part 134.
226. gbest135.seq - EST (expressed sequence tag) sequence entries, part 135.
227. gbest136.seq - EST (expressed sequence tag) sequence entries, part 136.
228. gbest137.seq - EST (expressed sequence tag) sequence entries, part 137.
229. gbest138.seq - EST (expressed sequence tag) sequence entries, part 138.
230. gbest139.seq - EST (expressed sequence tag) sequence entries, part 139.
231. gbest140.seq - EST (expressed sequence tag) sequence entries, part 140.
232. gbest141.seq - EST (expressed sequence tag) sequence entries, part 141.
233. gbest142.seq - EST (expressed sequence tag) sequence entries, part 142.
234. gbest143.seq - EST (expressed sequence tag) sequence entries, part 143.
235. gbest144.seq - EST (expressed sequence tag) sequence entries, part 144.
236. gbest145.seq - EST (expressed sequence tag) sequence entries, part 145.
237. gbest146.seq - EST (expressed sequence tag) sequence entries, part 146.
238. gbest147.seq - EST (expressed sequence tag) sequence entries, part 147.
239. gbest148.seq - EST (expressed sequence tag) sequence entries, part 148.
240. gbest149.seq - EST (expressed sequence tag) sequence entries, part 149.
241. gbest150.seq - EST (expressed sequence tag) sequence entries, part 150.
242. gbest151.seq - EST (expressed sequence tag) sequence entries, part 151.
243. gbest152.seq - EST (expressed sequence tag) sequence entries, part 152.
244. gbest153.seq - EST (expressed sequence tag) sequence entries, part 153.
245. gbest154.seq - EST (expressed sequence tag) sequence entries, part 154.
246. gbest155.seq - EST (expressed sequence tag) sequence entries, part 155.
247. gbest156.seq - EST (expressed sequence tag) sequence entries, part 156.
248. gbest157.seq - EST (expressed sequence tag) sequence entries, part 157.
249. gbest158.seq - EST (expressed sequence tag) sequence entries, part 158.
250. gbest159.seq - EST (expressed sequence tag) sequence entries, part 159.
251. gbest160.seq - EST (expressed sequence tag) sequence entries, part 160.
252. gbest161.seq - EST (expressed sequence tag) sequence entries, part 161.
253. gbest162.seq - EST (expressed sequence tag) sequence entries, part 162.
254. gbest163.seq - EST (expressed sequence tag) sequence entries, part 163.
255. gbest164.seq - EST (expressed sequence tag) sequence entries, part 164.
256. gbest165.seq - EST (expressed sequence tag) sequence entries, part 165.
257. gbest166.seq - EST (expressed sequence tag) sequence entries, part 166.
258. gbest167.seq - EST (expressed sequence tag) sequence entries, part 167.
259. gbest168.seq - EST (expressed sequence tag) sequence entries, part 168.
260. gbest169.seq - EST (expressed sequence tag) sequence entries, part 169.
261. gbest170.seq - EST (expressed sequence tag) sequence entries, part 170.
262. gbest171.seq - EST (expressed sequence tag) sequence entries, part 171.
263. gbest172.seq - EST (expressed sequence tag) sequence entries, part 172.
264. gbest173.seq - EST (expressed sequence tag) sequence entries, part 173.
265. gbest174.seq - EST (expressed sequence tag) sequence entries, part 174.
266. gbest175.seq - EST (expressed sequence tag) sequence entries, part 175.
267. gbest176.seq - EST (expressed sequence tag) sequence entries, part 176.
268. gbest177.seq - EST (expressed sequence tag) sequence entries, part 177.
269. gbest178.seq - EST (expressed sequence tag) sequence entries, part 178.
270. gbest179.seq - EST (expressed sequence tag) sequence entries, part 179.
271. gbest180.seq - EST (expressed sequence tag) sequence entries, part 180.
272. gbest181.seq - EST (expressed sequence tag) sequence entries, part 181.
273. gbest182.seq - EST (expressed sequence tag) sequence entries, part 182.
274. gbest183.seq - EST (expressed sequence tag) sequence entries, part 183.
275. gbest184.seq - EST (expressed sequence tag) sequence entries, part 184.
276. gbest185.seq - EST (expressed sequence tag) sequence entries, part 185.
277. gbest186.seq - EST (expressed sequence tag) sequence entries, part 186.
278. gbest187.seq - EST (expressed sequence tag) sequence entries, part 187.
279. gbest188.seq - EST (expressed sequence tag) sequence entries, part 188.
280. gbest189.seq - EST (expressed sequence tag) sequence entries, part 189.
281. gbest190.seq - EST (expressed sequence tag) sequence entries, part 190.
282. gbest191.seq - EST (expressed sequence tag) sequence entries, part 191.
283. gbest192.seq - EST (expressed sequence tag) sequence entries, part 192.
284. gbest193.seq - EST (expressed sequence tag) sequence entries, part 193.
285. gbest194.seq - EST (expressed sequence tag) sequence entries, part 194.
286. gbest195.seq - EST (expressed sequence tag) sequence entries, part 195.
287. gbest196.seq - EST (expressed sequence tag) sequence entries, part 196.
288. gbest197.seq - EST (expressed sequence tag) sequence entries, part 197.
289. gbest198.seq - EST (expressed sequence tag) sequence entries, part 198.
290. gbest199.seq - EST (expressed sequence tag) sequence entries, part 199.
291. gbest200.seq - EST (expressed sequence tag) sequence entries, part 200.
292. gbest201.seq - EST (expressed sequence tag) sequence entries, part 201.
293. gbest202.seq - EST (expressed sequence tag) sequence entries, part 202.
294. gbest203.seq - EST (expressed sequence tag) sequence entries, part 203.
295. gbest204.seq - EST (expressed sequence tag) sequence entries, part 204.
296. gbest205.seq - EST (expressed sequence tag) sequence entries, part 205.
297. gbest206.seq - EST (expressed sequence tag) sequence entries, part 206.
298. gbest207.seq - EST (expressed sequence tag) sequence entries, part 207.
299. gbest208.seq - EST (expressed sequence tag) sequence entries, part 208.
300. gbest209.seq - EST (expressed sequence tag) sequence entries, part 209.
301. gbest210.seq - EST (expressed sequence tag) sequence entries, part 210.
302. gbest211.seq - EST (expressed sequence tag) sequence entries, part 211.
303. gbest212.seq - EST (expressed sequence tag) sequence entries, part 212.
304. gbest213.seq - EST (expressed sequence tag) sequence entries, part 213.
305. gbest214.seq - EST (expressed sequence tag) sequence entries, part 214.
306. gbest215.seq - EST (expressed sequence tag) sequence entries, part 215.
307. gbest216.seq - EST (expressed sequence tag) sequence entries, part 216.
308. gbest217.seq - EST (expressed sequence tag) sequence entries, part 217.
309. gbest218.seq - EST (expressed sequence tag) sequence entries, part 218.
310. gbest219.seq - EST (expressed sequence tag) sequence entries, part 219.
311. gbest220.seq - EST (expressed sequence tag) sequence entries, part 220.
312. gbest221.seq - EST (expressed sequence tag) sequence entries, part 221.
313. gbest222.seq - EST (expressed sequence tag) sequence entries, part 222.
314. gbest223.seq - EST (expressed sequence tag) sequence entries, part 223.
315. gbest224.seq - EST (expressed sequence tag) sequence entries, part 224.
316. gbest225.seq - EST (expressed sequence tag) sequence entries, part 225.
317. gbest226.seq - EST (expressed sequence tag) sequence entries, part 226.
318. gbest227.seq - EST (expressed sequence tag) sequence entries, part 227.
319. gbest228.seq - EST (expressed sequence tag) sequence entries, part 228.
320. gbest229.seq - EST (expressed sequence tag) sequence entries, part 229.
321. gbest230.seq - EST (expressed sequence tag) sequence entries, part 230.
322. gbest231.seq - EST (expressed sequence tag) sequence entries, part 231.
323. gbest232.seq - EST (expressed sequence tag) sequence entries, part 232.
324. gbest233.seq - EST (expressed sequence tag) sequence entries, part 233.
325. gbest234.seq - EST (expressed sequence tag) sequence entries, part 234.
326. gbest235.seq - EST (expressed sequence tag) sequence entries, part 235.
327. gbest236.seq - EST (expressed sequence tag) sequence entries, part 236.
328. gbest237.seq - EST (expressed sequence tag) sequence entries, part 237.
329. gbest238.seq - EST (expressed sequence tag) sequence entries, part 238.
330. gbest239.seq - EST (expressed sequence tag) sequence entries, part 239.
331. gbest240.seq - EST (expressed sequence tag) sequence entries, part 240.
332. gbest241.seq - EST (expressed sequence tag) sequence entries, part 241.
333. gbest242.seq - EST (expressed sequence tag) sequence entries, part 242.
334. gbest243.seq - EST (expressed sequence tag) sequence entries, part 243.
335. gbest244.seq - EST (expressed sequence tag) sequence entries, part 244.
336. gbest245.seq - EST (expressed sequence tag) sequence entries, part 245.
337. gbest246.seq - EST (expressed sequence tag) sequence entries, part 246.
338. gbest247.seq - EST (expressed sequence tag) sequence entries, part 247.
339. gbest248.seq - EST (expressed sequence tag) sequence entries, part 248.
340. gbest249.seq - EST (expressed sequence tag) sequence entries, part 249.
341. gbest250.seq - EST (expressed sequence tag) sequence entries, part 250.
342. gbest251.seq - EST (expressed sequence tag) sequence entries, part 251.
343. gbest252.seq - EST (expressed sequence tag) sequence entries, part 252.
344. gbest253.seq - EST (expressed sequence tag) sequence entries, part 253.
345. gbest254.seq - EST (expressed sequence tag) sequence entries, part 254.
346. gbest255.seq - EST (expressed sequence tag) sequence entries, part 255.
347. gbest256.seq - EST (expressed sequence tag) sequence entries, part 256.
348. gbest257.seq - EST (expressed sequence tag) sequence entries, part 257.
349. gbest258.seq - EST (expressed sequence tag) sequence entries, part 258.
350. gbest259.seq - EST (expressed sequence tag) sequence entries, part 259.
351. gbpat1.seq - Patent sequence entries, part 1.
352. gbpat2.seq - Patent sequence entries, part 2.
353. gbpat3.seq - Patent sequence entries, part 3.
354. gbpat4.seq - Patent sequence entries, part 4.
355. gbpat5.seq - Patent sequence entries, part 5.
356. gbpat6.seq - Patent sequence entries, part 6.
357. gbpat7.seq - Patent sequence entries, part 7.
358. gbpat8.seq - Patent sequence entries, part 8.
359. gbsts1.seq - STS (sequence tagged site) sequence entries, part 1.
360. gbsts2.seq - STS (sequence tagged site) sequence entries, part 2.
361. gbsts3.seq - STS (sequence tagged site) sequence entries, part 3.
362. gbgss1.seq - GSS (genome survey sequence) sequence entries, part 1.
363. gbgss2.seq - GSS (genome survey sequence) sequence entries, part 2.
364. gbgss3.seq - GSS (genome survey sequence) sequence entries, part 3.
365. gbgss4.seq - GSS (genome survey sequence) sequence entries, part 4.
366. gbgss5.seq - GSS (genome survey sequence) sequence entries, part 5.
367. gbgss6.seq - GSS (genome survey sequence) sequence entries, part 6.
368. gbgss7.seq - GSS (genome survey sequence) sequence entries, part 7.
369. gbgss8.seq - GSS (genome survey sequence) sequence entries, part 8.
370. gbgss9.seq - GSS (genome survey sequence) sequence entries, part 9.
371. gbgss10.seq - GSS (genome survey sequence) sequence entries, part 10.
372. gbgss11.seq - GSS (genome survey sequence) sequence entries, part 11.
373. gbgss12.seq - GSS (genome survey sequence) sequence entries, part 12.
374. gbgss13.seq - GSS (genome survey sequence) sequence entries, part 13.
375. gbgss14.seq - GSS (genome survey sequence) sequence entries, part 14.
376. gbgss15.seq - GSS (genome survey sequence) sequence entries, part 15.
377. gbgss16.seq - GSS (genome survey sequence) sequence entries, part 16.
378. gbgss17.seq - GSS (genome survey sequence) sequence entries, part 17.
379. gbgss18.seq - GSS (genome survey sequence) sequence entries, part 18.
380. gbgss19.seq - GSS (genome survey sequence) sequence entries, part 19.
381. gbgss20.seq - GSS (genome survey sequence) sequence entries, part 20.
382. gbgss21.seq - GSS (genome survey sequence) sequence entries, part 21.
383. gbgss22.seq - GSS (genome survey sequence) sequence entries, part 22.
384. gbgss23.seq - GSS (genome survey sequence) sequence entries, part 23.
385. gbgss24.seq - GSS (genome survey sequence) sequence entries, part 24.
386. gbgss25.seq - GSS (genome survey sequence) sequence entries, part 25.
387. gbgss26.seq - GSS (genome survey sequence) sequence entries, part 26.
388. gbgss27.seq - GSS (genome survey sequence) sequence entries, part 27.
389. gbgss28.seq - GSS (genome survey sequence) sequence entries, part 28.
390. gbgss29.seq - GSS (genome survey sequence) sequence entries, part 29.
391. gbgss30.seq - GSS (genome survey sequence) sequence entries, part 30.
392. gbgss31.seq - GSS (genome survey sequence) sequence entries, part 31.
393. gbgss32.seq - GSS (genome survey sequence) sequence entries, part 32.
394. gbgss33.seq - GSS (genome survey sequence) sequence entries, part 33.
395. gbgss34.seq - GSS (genome survey sequence) sequence entries, part 34.
396. gbgss35.seq - GSS (genome survey sequence) sequence entries, part 35.
397. gbgss36.seq - GSS (genome survey sequence) sequence entries, part 36.
398. gbgss37.seq - GSS (genome survey sequence) sequence entries, part 37.
399. gbgss38.seq - GSS (genome survey sequence) sequence entries, part 38.
400. gbgss39.seq - GSS (genome survey sequence) sequence entries, part 39.
401. gbgss40.seq - GSS (genome survey sequence) sequence entries, part 40.
402. gbgss41.seq - GSS (genome survey sequence) sequence entries, part 41.
403. gbgss42.seq - GSS (genome survey sequence) sequence entries, part 42.
404. gbgss43.seq - GSS (genome survey sequence) sequence entries, part 43.
405. gbgss44.seq - GSS (genome survey sequence) sequence entries, part 44.
406. gbgss45.seq - GSS (genome survey sequence) sequence entries, part 45.
407. gbgss46.seq - GSS (genome survey sequence) sequence entries, part 46.
408. gbgss47.seq - GSS (genome survey sequence) sequence entries, part 47.
409. gbgss48.seq - GSS (genome survey sequence) sequence entries, part 48.
410. gbgss49.seq - GSS (genome survey sequence) sequence entries, part 49.
411. gbgss50.seq - GSS (genome survey sequence) sequence entries, part 50.
412. gbgss51.seq - GSS (genome survey sequence) sequence entries, part 51.
413. gbgss52.seq - GSS (genome survey sequence) sequence entries, part 52.
414. gbgss53.seq - GSS (genome survey sequence) sequence entries, part 53.
415. gbgss54.seq - GSS (genome survey sequence) sequence entries, part 54.
416. gbgss55.seq - GSS (genome survey sequence) sequence entries, part 55.
417. gbgss56.seq - GSS (genome survey sequence) sequence entries, part 56.
418. gbgss57.seq - GSS (genome survey sequence) sequence entries, part 57.
419. gbgss58.seq - GSS (genome survey sequence) sequence entries, part 58.
420. gbgss59.seq - GSS (genome survey sequence) sequence entries, part 59.
421. gbgss60.seq - GSS (genome survey sequence) sequence entries, part 60.
422. gbgss61.seq - GSS (genome survey sequence) sequence entries, part 61.
423. gbgss62.seq - GSS (genome survey sequence) sequence entries, part 62.
424. gbgss63.seq - GSS (genome survey sequence) sequence entries, part 63.
425. gbgss64.seq - GSS (genome survey sequence) sequence entries, part 64.
426. gbgss65.seq - GSS (genome survey sequence) sequence entries, part 65.
427. gbgss66.seq - GSS (genome survey sequence) sequence entries, part 66.
428. gbgss67.seq - GSS (genome survey sequence) sequence entries, part 67.
429. gbgss68.seq - GSS (genome survey sequence) sequence entries, part 68.
430. gbgss69.seq - GSS (genome survey sequence) sequence entries, part 69.
431. gbgss70.seq - GSS (genome survey sequence) sequence entries, part 70.
432. gbgss71.seq - GSS (genome survey sequence) sequence entries, part 71.
433. gbgss72.seq - GSS (genome survey sequence) sequence entries, part 72.
434. gbgss73.seq - GSS (genome survey sequence) sequence entries, part 73.
435. gbgss74.seq - GSS (genome survey sequence) sequence entries, part 74.
436. gbgss75.seq - GSS (genome survey sequence) sequence entries, part 75.
437. gbgss76.seq - GSS (genome survey sequence) sequence entries, part 76.
438. gbgss77.seq - GSS (genome survey sequence) sequence entries, part 77.
439. gbhtg1.seq - HTGS (high throughput genomic sequencing) sequence entries, part 1.
440. gbhtg2.seq - HTGS (high throughput genomic sequencing) sequence entries, part 2.
441. gbhtg3.seq - HTGS (high throughput genomic sequencing) sequence entries, part 3.
442. gbhtg4.seq - HTGS (high throughput genomic sequencing) sequence entries, part 4.
443. gbhtg5.seq - HTGS (high throughput genomic sequencing) sequence entries, part 5.
444. gbhtg6.seq - HTGS (high throughput genomic sequencing) sequence entries, part 6.
445. gbhtg7.seq - HTGS (high throughput genomic sequencing) sequence entries, part 7.
446. gbhtg8.seq - HTGS (high throughput genomic sequencing) sequence entries, part 8.
447. gbhtg9.seq - HTGS (high throughput genomic sequencing) sequence entries, part 9.
448. gbhtg10.seq - HTGS (high throughput genomic sequencing) sequence entries, part 10.
449. gbhtg11.seq - HTGS (high throughput genomic sequencing) sequence entries, part 11.
450. gbhtg12.seq - HTGS (high throughput genomic sequencing) sequence entries, part 12.
451. gbhtg13.seq - HTGS (high throughput genomic sequencing) sequence entries, part 13.
452. gbhtg14.seq - HTGS (high throughput genomic sequencing) sequence entries, part 14.
453. gbhtg15.seq - HTGS (high throughput genomic sequencing) sequence entries, part 15.
454. gbhtg16.seq - HTGS (high throughput genomic sequencing) sequence entries, part 16.
455. gbhtg17.seq - HTGS (high throughput genomic sequencing) sequence entries, part 17.
456. gbhtg18.seq - HTGS (high throughput genomic sequencing) sequence entries, part 18.
457. gbhtg19.seq - HTGS (high throughput genomic sequencing) sequence entries, part 19.
458. gbhtg20.seq - HTGS (high throughput genomic sequencing) sequence entries, part 20.
459. gbhtg21.seq - HTGS (high throughput genomic sequencing) sequence entries, part 21.
460. gbhtg22.seq - HTGS (high throughput genomic sequencing) sequence entries, part 22.
461. gbhtg23.seq - HTGS (high throughput genomic sequencing) sequence entries, part 23.
462. gbhtg24.seq - HTGS (high throughput genomic sequencing) sequence entries, part 24.
463. gbhtg25.seq - HTGS (high throughput genomic sequencing) sequence entries, part 25.
464. gbhtg26.seq - HTGS (high throughput genomic sequencing) sequence entries, part 26.
465. gbhtg27.seq - HTGS (high throughput genomic sequencing) sequence entries, part 27.
466. gbhtg28.seq - HTGS (high throughput genomic sequencing) sequence entries, part 28.
467. gbhtg29.seq - HTGS (high throughput genomic sequencing) sequence entries, part 29.
468. gbhtg30.seq - HTGS (high throughput genomic sequencing) sequence entries, part 30.
469. gbhtg31.seq - HTGS (high throughput genomic sequencing) sequence entries, part 31.
470. gbhtg32.seq - HTGS (high throughput genomic sequencing) sequence entries, part 32.
471. gbhtg33.seq - HTGS (high throughput genomic sequencing) sequence entries, part 33.
472. gbhtg34.seq - HTGS (high throughput genomic sequencing) sequence entries, part 34.
473. gbhtg35.seq - HTGS (high throughput genomic sequencing) sequence entries, part 35.
474. gbhtg36.seq - HTGS (high throughput genomic sequencing) sequence entries, part 36.
475. gbhtg37.seq - HTGS (high throughput genomic sequencing) sequence entries, part 37.
476. gbhtg38.seq - HTGS (high throughput genomic sequencing) sequence entries, part 38.
477. gbhtg39.seq - HTGS (high throughput genomic sequencing) sequence entries, part 39.
478. gbhtg40.seq - HTGS (high throughput genomic sequencing) sequence entries, part 40.
479. gbhtg41.seq - HTGS (high throughput genomic sequencing) sequence entries, part 41.
480. gbhtg42.seq - HTGS (high throughput genomic sequencing) sequence entries, part 42.
481. gbhtg43.seq - HTGS (high throughput genomic sequencing) sequence entries, part 43.
482. gbhtg44.seq - HTGS (high throughput genomic sequencing) sequence entries, part 44.
483. gbhtg45.seq - HTGS (high throughput genomic sequencing) sequence entries, part 45.
484. gbhtg46.seq - HTGS (high throughput genomic sequencing) sequence entries, part 46.
485. gbhtg47.seq - HTGS (high throughput genomic sequencing) sequence entries, part 47.
486. gbhtg48.seq - HTGS (high throughput genomic sequencing) sequence entries, part 48.
487. gbhtg49.seq - HTGS (high throughput genomic sequencing) sequence entries, part 49.
488. gbhtg50.seq - HTGS (high throughput genomic sequencing) sequence entries, part 50.
489. gbhtg51.seq - HTGS (high throughput genomic sequencing) sequence entries, part 51.
490. gbhtg52.seq - HTGS (high throughput genomic sequencing) sequence entries, part 52.
491. gbhtg53.seq - HTGS (high throughput genomic sequencing) sequence entries, part 53.
492. gbhtg54.seq - HTGS (high throughput genomic sequencing) sequence entries, part 54.
493. gbhtg55.seq - HTGS (high throughput genomic sequencing) sequence entries, part 55.
494. gbhtg56.seq - HTGS (high throughput genomic sequencing) sequence entries, part 56.
495. gbhtg57.seq - HTGS (high throughput genomic sequencing) sequence entries, part 57.
496. gbhtg58.seq - HTGS (high throughput genomic sequencing) sequence entries, part 58.
497. gbhtg59.seq - HTGS (high throughput genomic sequencing) sequence entries, part 59.
498. gbhtg60.seq - HTGS (high throughput genomic sequencing) sequence entries, part 60.
499. gbhtg61.seq - HTGS (high throughput genomic sequencing) sequence entries, part 61.
500. gbhtg62.seq - HTGS (high throughput genomic sequencing) sequence entries, part 62.
501. gbhtc1.seq - HTC (high throughput cDNA sequencing) entries, part 1.
502. gbhtc2.seq - HTC (high throughput cDNA sequencing) entries, part 2.
503. gbhtc3.seq - HTC (high throughput cDNA sequencing) entries, part 3.
504. gbhtc4.seq - HTC (high throughput cDNA sequencing) entries, part 4.
505. gbcon.seq - CON division entries (see description below for details)
506. gbchg.txt - Accession numbers of entries updated since the previous release.
507. gbdel.txt - Accession numbers of entries deleted since the previous release.
508. gbnew.txt - Accession numbers of entries new since the previous release.
The gbcon.seq data file provides an alternative representation for complex
sequences, such as segmented sets and complete-genomes that have been split
into pieces. These "CON" records do not contain sequence data; they utilize
a CONTIG linetype with a join() statement which describes how the component
sequences can be assembled to form the larger sequence. The contents of the
CON division are not reflected in the 'index' files that accompany GenBank
releases. The GenBank README describes the CON division of GenBank in more
detail:
ftp://ftp.ncbi.nih.gov/genbank/README.genbank
2.2.5 File Sizes
Uncompressed, the Release 136.0 flatfiles require roughly 107 GB (sequence
files only) or 121 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
837134383 gbacc.idx
502699314 gbaut1.idx
515535817 gbaut10.idx
501018036 gbaut11.idx
512839553 gbaut12.idx
504936250 gbaut13.idx
505868038 gbaut14.idx
506294552 gbaut15.idx
500555716 gbaut16.idx
500095474 gbaut17.idx
500943728 gbaut18.idx
501784667 gbaut19.idx
523706957 gbaut2.idx
108409392 gbaut20.idx
500266486 gbaut3.idx
502018927 gbaut4.idx
501814192 gbaut5.idx
515591984 gbaut6.idx
504947626 gbaut7.idx
526153114 gbaut8.idx
500163019 gbaut9.idx
250010905 gbbct1.seq
250003043 gbbct2.seq
250013085 gbbct3.seq
250080136 gbbct4.seq
250336369 gbbct5.seq
250208632 gbbct6.seq
135306823 gbbct7.seq
1379073 gbchg.txt
17304010 gbcon.seq
38687 gbdel.txt
230688764 gbest1.seq
230689141 gbest10.seq
230687612 gbest100.seq
230690244 gbest101.seq
230689576 gbest102.seq
230689079 gbest103.seq
230687664 gbest104.seq
230689062 gbest105.seq
230689548 gbest106.seq
230689122 gbest107.seq
230690092 gbest108.seq
230687577 gbest109.seq
230688439 gbest11.seq
230688628 gbest110.seq
230688418 gbest111.seq
230689455 gbest112.seq
230689189 gbest113.seq
230690358 gbest114.seq
230689216 gbest115.seq
230690009 gbest116.seq
230689642 gbest117.seq
230688134 gbest118.seq
230689201 gbest119.seq
230690295 gbest12.seq
230687648 gbest120.seq
230688101 gbest121.seq
230690118 gbest122.seq
230688684 gbest123.seq
230688985 gbest124.seq
230689952 gbest125.seq
230691612 gbest126.seq
230688547 gbest127.seq
230691005 gbest128.seq
230688125 gbest129.seq
230688897 gbest13.seq
230690294 gbest130.seq
230689960 gbest131.seq
230687724 gbest132.seq
230687525 gbest133.seq
230687797 gbest134.seq
230689488 gbest135.seq
230690829 gbest136.seq
230687884 gbest137.seq
230690522 gbest138.seq
230689169 gbest139.seq
230689346 gbest14.seq
230687892 gbest140.seq
230687993 gbest141.seq
230689479 gbest142.seq
230690185 gbest143.seq
230690103 gbest144.seq
230690604 gbest145.seq
230691654 gbest146.seq
230688710 gbest147.seq
230688834 gbest148.seq
230689437 gbest149.seq
230689583 gbest15.seq
230691754 gbest150.seq
230689393 gbest151.seq
230689526 gbest152.seq
230690776 gbest153.seq
230690685 gbest154.seq
230690946 gbest155.seq
230687851 gbest156.seq
230690663 gbest157.seq
230689272 gbest158.seq
230687481 gbest159.seq
230687919 gbest16.seq
230690908 gbest160.seq
230693194 gbest161.seq
230688033 gbest162.seq
230689103 gbest163.seq
230688985 gbest164.seq
230691142 gbest165.seq
230690364 gbest166.seq
230690586 gbest167.seq
230689107 gbest168.seq
230689259 gbest169.seq
230688196 gbest17.seq
230690617 gbest170.seq
230688082 gbest171.seq
230689004 gbest172.seq
230688933 gbest173.seq
230688201 gbest174.seq
230688724 gbest175.seq
230688091 gbest176.seq
230690432 gbest177.seq
230687850 gbest178.seq
230687535 gbest179.seq
230688201 gbest18.seq
230689118 gbest180.seq
230690501 gbest181.seq
230688018 gbest182.seq
230689899 gbest183.seq
230688991 gbest184.seq
230688902 gbest185.seq
230688681 gbest186.seq
230689031 gbest187.seq
230689227 gbest188.seq
230689689 gbest189.seq
230688413 gbest19.seq
230687618 gbest190.seq
230687489 gbest191.seq
230689447 gbest192.seq
230689160 gbest193.seq
230689164 gbest194.seq
164856125 gbest195.seq
163881188 gbest196.seq
170575915 gbest197.seq
169905190 gbest198.seq
169903052 gbest199.seq
230690279 gbest2.seq
230688593 gbest20.seq
167046057 gbest200.seq
166681788 gbest201.seq
166304698 gbest202.seq
166230399 gbest203.seq
166200774 gbest204.seq
166293321 gbest205.seq
165230850 gbest206.seq
168737860 gbest207.seq
165586571 gbest208.seq
163966490 gbest209.seq
230688915 gbest21.seq
166895063 gbest210.seq
170508437 gbest211.seq
168397690 gbest212.seq
167343855 gbest213.seq
167558955 gbest214.seq
166906761 gbest215.seq
166533484 gbest216.seq
166127302 gbest217.seq
166427307 gbest218.seq
166980994 gbest219.seq
230687622 gbest22.seq
175271776 gbest220.seq
178632934 gbest221.seq
183036038 gbest222.seq
230689987 gbest223.seq
230691465 gbest224.seq
230688370 gbest225.seq
230689418 gbest226.seq
230687463 gbest227.seq
230689276 gbest228.seq
230688769 gbest229.seq
230688626 gbest23.seq
230689479 gbest230.seq
230688999 gbest231.seq
230691397 gbest232.seq
230687524 gbest233.seq
230690292 gbest234.seq
230688998 gbest235.seq
230690515 gbest236.seq
230688030 gbest237.seq
230687887 gbest238.seq
230688266 gbest239.seq
230687620 gbest24.seq
230689904 gbest240.seq
230689088 gbest241.seq
230688231 gbest242.seq
230688837 gbest243.seq
230687557 gbest244.seq
230688160 gbest245.seq
230688192 gbest246.seq
230689693 gbest247.seq
230690297 gbest248.seq
230689797 gbest249.seq
230689547 gbest25.seq
230687755 gbest250.seq
230689143 gbest251.seq
230687727 gbest252.seq
230688834 gbest253.seq
230690149 gbest254.seq
230690042 gbest255.seq
227185842 gbest256.seq
230687599 gbest257.seq
230690218 gbest258.seq
13742954 gbest259.seq
230690174 gbest26.seq
230689661 gbest27.seq
230687872 gbest28.seq
230688499 gbest29.seq
230689250 gbest3.seq
230688726 gbest30.seq
230688649 gbest31.seq
230687941 gbest32.seq
230689424 gbest33.seq
230690142 gbest34.seq
230687816 gbest35.seq
224806024 gbest36.seq
193801286 gbest37.seq
193636564 gbest38.seq
219519512 gbest39.seq
230689601 gbest4.seq
217927409 gbest40.seq
217613573 gbest41.seq
218633007 gbest42.seq
230689983 gbest43.seq
230688915 gbest44.seq
227838583 gbest45.seq
230688411 gbest46.seq
230689535 gbest47.seq
230687572 gbest48.seq
230689802 gbest49.seq
169257428 gbest5.seq
230689659 gbest50.seq
230689320 gbest51.seq
230687713 gbest52.seq
230687601 gbest53.seq
230690040 gbest54.seq
230689628 gbest55.seq
230687790 gbest56.seq
230687543 gbest57.seq
230688406 gbest58.seq
230690176 gbest59.seq
179384841 gbest6.seq
230689524 gbest60.seq
230687524 gbest61.seq
211159475 gbest62.seq
210838476 gbest63.seq
209767776 gbest64.seq
210604135 gbest65.seq
211373967 gbest66.seq
211585026 gbest67.seq
210793443 gbest68.seq
210091849 gbest69.seq
230687991 gbest7.seq
211617710 gbest70.seq
209527921 gbest71.seq
206863456 gbest72.seq
209901600 gbest73.seq
209656580 gbest74.seq
213267312 gbest75.seq
227834487 gbest76.seq
230692408 gbest77.seq
230692708 gbest78.seq
223100265 gbest79.seq
230689953 gbest8.seq
214794558 gbest80.seq
215488344 gbest81.seq
230688767 gbest82.seq
230688511 gbest83.seq
230691075 gbest84.seq
230689737 gbest85.seq
230688927 gbest86.seq
230689163 gbest87.seq
230687582 gbest88.seq
230689653 gbest89.seq
230688210 gbest9.seq
230688862 gbest90.seq
230690043 gbest91.seq
230688622 gbest92.seq
230688083 gbest93.seq
230688266 gbest94.seq
230687753 gbest95.seq
230688512 gbest96.seq
230690029 gbest97.seq
230688468 gbest98.seq
230690703 gbest99.seq
29596028 gbgen.idx
209718179 gbgss1.seq
209718531 gbgss10.seq
209716348 gbgss11.seq
209716154 gbgss12.seq
209717940 gbgss13.seq
209717605 gbgss14.seq
209716541 gbgss15.seq
209719113 gbgss16.seq
209718278 gbgss17.seq
209718190 gbgss18.seq
209719274 gbgss19.seq
209715935 gbgss2.seq
209718422 gbgss20.seq
209719050 gbgss21.seq
209719004 gbgss22.seq
209716818 gbgss23.seq
209719327 gbgss24.seq
209716303 gbgss25.seq
209718558 gbgss26.seq
209716784 gbgss27.seq
209716336 gbgss28.seq
209716269 gbgss29.seq
209716877 gbgss3.seq
209716250 gbgss30.seq
209717502 gbgss31.seq
209717544 gbgss32.seq
209716560 gbgss33.seq
209717047 gbgss34.seq
209716779 gbgss35.seq
209716660 gbgss36.seq
209716692 gbgss37.seq
209719366 gbgss38.seq
209717886 gbgss39.seq
209718222 gbgss4.seq
209716681 gbgss40.seq
209717271 gbgss41.seq
209716761 gbgss42.seq
209717831 gbgss43.seq
209716945 gbgss44.seq
209717019 gbgss45.seq
209718635 gbgss46.seq
209717940 gbgss47.seq
209719110 gbgss48.seq
209716295 gbgss49.seq
209716630 gbgss5.seq
209716410 gbgss50.seq
209718234 gbgss51.seq
209716107 gbgss52.seq
209716387 gbgss53.seq
209716081 gbgss54.seq
209716639 gbgss55.seq
209717500 gbgss56.seq
209716885 gbgss57.seq
209716112 gbgss58.seq
209718632 gbgss59.seq
209716624 gbgss6.seq
209717101 gbgss60.seq
209718506 gbgss61.seq
209716636 gbgss62.seq
209718416 gbgss63.seq
209718957 gbgss64.seq
209718469 gbgss65.seq
204005474 gbgss66.seq
250001072 gbgss67.seq
250002580 gbgss68.seq
250001187 gbgss69.seq
209717618 gbgss7.seq
250001419 gbgss70.seq
250000314 gbgss71.seq
250001011 gbgss72.seq
250002962 gbgss73.seq
250000973 gbgss74.seq
250004479 gbgss75.seq
250001174 gbgss76.seq
136274408 gbgss77.seq
209718415 gbgss8.seq
209717938 gbgss9.seq
250006506 gbhtc1.seq
250009284 gbhtc2.seq
250001133 gbhtc3.seq
76968070 gbhtc4.seq
250124857 gbhtg1.seq
250043650 gbhtg10.seq
250131574 gbhtg11.seq
250188017 gbhtg12.seq
250265882 gbhtg13.seq
250309818 gbhtg14.seq
250142756 gbhtg15.seq
250005959 gbhtg16.seq
250030151 gbhtg17.seq
250026997 gbhtg18.seq
250160065 gbhtg19.seq
250005446 gbhtg2.seq
250167867 gbhtg20.seq
250240494 gbhtg21.seq
250233491 gbhtg22.seq
250053555 gbhtg23.seq
250021421 gbhtg24.seq
250106271 gbhtg25.seq
250050956 gbhtg26.seq
250213395 gbhtg27.seq
250209526 gbhtg28.seq
250002450 gbhtg29.seq
250005079 gbhtg3.seq
250155472 gbhtg30.seq
250235924 gbhtg31.seq
250149589 gbhtg32.seq
250105799 gbhtg33.seq
250028146 gbhtg34.seq
250037426 gbhtg35.seq
250172553 gbhtg36.seq
250055415 gbhtg37.seq
250181718 gbhtg38.seq
250094263 gbhtg39.seq
250005353 gbhtg4.seq
250160332 gbhtg40.seq
250014144 gbhtg41.seq
250087213 gbhtg42.seq
250073368 gbhtg43.seq
250037358 gbhtg44.seq
250045844 gbhtg45.seq
250145400 gbhtg46.seq
250266774 gbhtg47.seq
250308786 gbhtg48.seq
250226200 gbhtg49.seq
250156736 gbhtg5.seq
250150656 gbhtg50.seq
250025363 gbhtg51.seq
250007416 gbhtg52.seq
250151097 gbhtg53.seq
250077597 gbhtg54.seq
250034042 gbhtg55.seq
250105047 gbhtg56.seq
250083943 gbhtg57.seq
250037453 gbhtg58.seq
250062729 gbhtg59.seq
250004956 gbhtg6.seq
250043427 gbhtg60.seq
250196819 gbhtg61.seq
201370908 gbhtg62.seq
250070570 gbhtg7.seq
250031766 gbhtg8.seq
250028479 gbhtg9.seq
250079440 gbinv1.seq
250004406 gbinv2.seq
250002569 gbinv3.seq
250050265 gbinv4.seq
250037723 gbinv5.seq
44746650 gbinv6.seq
643215606 gbjou.idx
572971194 gbkey.idx
174608132 gbmam.seq
24196618 gbnew.txt
250001237 gbpat1.seq
250001594 gbpat2.seq
250000237 gbpat3.seq
250000079 gbpat4.seq
250000266 gbpat5.seq
250001578 gbpat6.seq
250000292 gbpat7.seq
196827803 gbpat8.seq
22767396 gbphg.seq
250014776 gbpln1.seq
250001119 gbpln2.seq
250002809 gbpln3.seq
250186720 gbpln4.seq
250000261 gbpln5.seq
250143334 gbpln6.seq
250008056 gbpln7.seq
83711429 gbpln8.seq
250299169 gbpri1.seq
250051725 gbpri10.seq
250160370 gbpri11.seq
250084597 gbpri12.seq
250153360 gbpri13.seq
250009652 gbpri14.seq
250005159 gbpri15.seq
250122528 gbpri16.seq
250090188 gbpri17.seq
250083547 gbpri18.seq
250016269 gbpri19.seq
250236012 gbpri2.seq
250155090 gbpri20.seq
250077644 gbpri21.seq
250275246 gbpri22.seq
250000519 gbpri23.seq
250001726 gbpri24.seq
196945937 gbpri25.seq
250161625 gbpri3.seq
250074005 gbpri4.seq
250145498 gbpri5.seq
250150787 gbpri6.seq
250062188 gbpri7.seq
250119306 gbpri8.seq
250013262 gbpri9.seq
159460 gbrel.txt
250202894 gbrod1.seq
250110177 gbrod2.seq
250011759 gbrod3.seq
250181843 gbrod4.seq
250010727 gbrod5.seq
250000056 gbrod6.seq
250001836 gbrod7.seq
87944468 gbrod8.seq
2047460704 gbsdr.txt
1490312 gbsec.idx
250002753 gbsts1.seq
250002101 gbsts2.seq
152781123 gbsts3.seq
45347218 gbsyn.seq
1453416 gbuna.seq
250002387 gbvrl1.seq
250000068 gbvrl2.seq
149661163 gbvrl3.seq
250011084 gbvrt1.seq
250000948 gbvrt2.seq
75980567 gbvrt3.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 22794 100188570
BCT2 8002 106514710
BCT3 32328 101468442
BCT4 37920 95117544
BCT5 35066 101977382
BCT6 34615 94022950
BCT7 22437 47998524
CON 11248 731564697
EST1 67661 26107820
EST10 76264 29590578
EST100 73852 33976829
EST101 69543 29284840
EST102 63800 30942416
EST103 67692 41287682
EST104 69551 36397578
EST105 69731 43976663
EST106 74914 33791178
EST107 73487 27360417
EST108 74842 25748327
EST109 72606 41505114
EST11 74361 28475538
EST110 63743 31149280
EST111 77918 48059062
EST112 78423 44278385
EST113 71982 44807156
EST114 68263 42489190
EST115 72442 46534998
EST116 67506 44786073
EST117 73303 43455256
EST118 74197 44865752
EST119 73164 47208997
EST12 76882 30566151
EST120 74314 48449268
EST121 72378 45398364
EST122 77512 40104999
EST123 74789 24207373
EST124 82247 46946810
EST125 74301 43758434
EST126 69929 41058779
EST127 66400 32581502
EST128 68302 38556522
EST129 66334 36624636
EST13 75737 28999588
EST130 67798 40277745
EST131 70552 40281953
EST132 71203 45643743
EST133 67679 41170485
EST134 72537 39514560
EST135 68636 41375217
EST136 58811 35549154
EST137 90761 48810724
EST138 97437 55799818
EST139 82148 42356430
EST14 77109 31093076
EST140 105054 56019356
EST141 106768 58116533
EST142 96843 53484436
EST143 77233 47264846
EST144 68137 34029146
EST145 63638 28928924
EST146 55105 25140315
EST147 63150 30677586
EST148 59747 30615269
EST149 64763 34626348
EST15 73821 30859589
EST150 74382 52454940
EST151 63689 43735633
EST152 80745 47525807
EST153 60541 30944028
EST154 61365 31020915
EST155 66501 40748296
EST156 65168 32124778
EST157 63717 46857086
EST158 81043 45290652
EST159 64087 41378583
EST16 75679 33425134
EST160 68108 38659886
EST161 60267 35410202
EST162 67540 43466518
EST163 68067 29843399
EST164 75979 33018742
EST165 68905 42899859
EST166 77638 38716328
EST167 63978 33281366
EST168 69319 49589277
EST169 68374 46197966
EST17 78445 31942356
EST170 67685 35852717
EST171 68895 44544173
EST172 68660 53087677
EST173 69028 35061475
EST174 69715 40984503
EST175 69636 59919123
EST176 64751 47866891
EST177 63294 46067400
EST178 62821 46548923
EST179 64798 45123647
EST18 83227 33663308
EST180 64673 46817061
EST181 63828 47007425
EST182 61767 39382996
EST183 62249 32681471
EST184 62925 36699416
EST185 85953 48324725
EST186 83036 54205039
EST187 72139 42519909
EST188 104109 65219768
EST189 106011 63993232
EST19 77563 31116465
EST190 104433 62213486
EST191 68650 38424585
EST192 68986 56211055
EST193 66294 68390854
EST194 59125 48717353
EST195 27863 10477315
EST196 27945 10484511
EST197 26830 9841980
EST198 26959 9498214
EST199 26994 9232352
EST2 74188 28480797
EST20 74005 31153576
EST200 27303 10221972
EST201 27248 9690407
EST202 27290 10182422
EST203 27278 11551253
EST204 27252 11478078
EST205 27299 10585320
EST206 27604 9562112
EST207 27063 8884682
EST208 27661 11239752
EST209 27945 10776527
EST21 74042 33173234
EST210 27492 11101581
EST211 26689 11773535
EST212 26939 11768507
EST213 27179 10609629
EST214 27021 11542864
EST215 27168 11774761
EST216 27303 11315993
EST217 27333 10801595
EST218 27294 10763826
EST219 27237 10606401
EST22 72484 30329518
EST220 25721 15756226
EST221 25129 16613849
EST222 38696 20615693
EST223 101866 41062506
EST224 71540 41513549
EST225 81628 45228787
EST226 62490 41096498
EST227 64625 34106590
EST228 74446 37962779
EST229 99890 46405715
EST23 77212 31982054
EST230 76094 42153732
EST231 65236 33480478
EST232 67812 32781630
EST233 68443 44887624
EST234 72908 34195187
EST235 70284 35632672
EST236 71221 46275777
EST237 63255 36699992
EST238 68277 33087635
EST239 86244 45946854
EST24 74627 32440626
EST240 76791 49953629
EST241 80956 54914414
EST242 95630 50996857
EST243 95420 43727767
EST244 74254 41159830
EST245 72833 40325473
EST246 71172 43428862
EST247 72199 47163378
EST248 69314 42663611
EST249 68605 40750608
EST25 75084 33285290
EST250 57902 41513005
EST251 91810 32813094
EST252 72587 25603703
EST253 71582 26710568
EST254 73170 25932353
EST255 72254 26263933
EST256 78234 26290938
EST257 71655 28567371
EST258 72569 27916755
EST259 5342 1803812
EST26 71649 29063534
EST27 75239 31960465
EST28 100032 47213739
EST29 74489 40291942
EST3 73150 29672764
EST30 64158 68665408
EST31 86562 49987605
EST32 94009 48092393
EST33 95955 48510511
EST34 100738 45552716
EST35 94900 51110113
EST36 91394 33587318
EST37 69274 18568027
EST38 69043 18418968
EST39 61711 18870730
EST4 73776 28103739
EST40 43539 11938243
EST41 43182 11884108
EST42 43061 11409286
EST43 80203 33041472
EST44 93652 42745755
EST45 91364 46761204
EST46 84588 40395417
EST47 104481 54613008
EST48 94193 46164180
EST49 76267 32773287
EST5 48950 15719349
EST50 66995 29515583
EST51 72226 31592732
EST52 69997 29339757
EST53 81317 32866665
EST54 74242 29785689
EST55 68190 27738006
EST56 65585 29233973
EST57 75587 34896673
EST58 74522 32995365
EST59 73859 28565544
EST6 54869 17285638
EST60 76509 27558486
EST61 82357 38363156
EST62 40258 11532675
EST63 40238 10972680
EST64 40252 12474456
EST65 40586 12583981
EST66 40621 12230191
EST67 40527 12895467
EST68 40375 12853329
EST69 40532 12087140
EST7 73802 29101214
EST70 40218 12058757
EST71 40975 12725468
EST72 41476 11875971
EST73 41172 13127517
EST74 41010 12995687
EST75 42608 12925005
EST76 44709 16127565
EST77 39859 25050207
EST78 41973 19950358
EST79 47741 19282620
EST8 75114 30210545
EST80 51472 23022383
EST81 51470 21683001
EST82 67639 30186658
EST83 70580 27318666
EST84 75056 29257320
EST85 74070 39451098
EST86 76894 41414072
EST87 77028 44284697
EST88 74924 34305403
EST89 74340 43323282
EST9 77197 29814817
EST90 70219 36034806
EST91 74676 33548839
EST92 72163 44544892
EST93 72592 33607385
EST94 72695 42872034
EST95 66550 35851506
EST96 72670 36291903
EST97 72584 47359332
EST98 72649 42639442
EST99 68552 46011133
GSS1 81470 34918090
GSS10 65105 33358374
GSS11 67816 39942304
GSS12 65974 32735100
GSS13 61597 33765322
GSS14 67585 35067112
GSS15 64316 30557917
GSS16 65668 28924204
GSS17 67459 35618411
GSS18 65847 38642487
GSS19 63414 29214883
GSS2 82768 34800392
GSS20 51838 26044204
GSS21 51793 26135551
GSS22 52466 24326398
GSS23 54960 23638842
GSS24 60386 39031600
GSS25 52641 23838110
GSS26 54225 34554986
GSS27 67804 34114383
GSS28 54385 20363946
GSS29 52380 24555529
GSS3 78298 37240711
GSS30 66852 30575722
GSS31 53357 28971683
GSS32 72490 36763325
GSS33 75740 35881891
GSS34 67497 36920082
GSS35 63483 43187962
GSS36 67684 32540430
GSS37 72345 38683327
GSS38 68574 36635018
GSS39 71867 40831470
GSS4 72885 37219390
GSS40 84305 55990291
GSS41 84266 54670931
GSS42 79692 41878017
GSS43 78673 44520682
GSS44 79764 34845536
GSS45 74300 27657438
GSS46 72708 51068468
GSS47 72300 51667781
GSS48 67045 45826781
GSS49 65242 43220110
GSS5 70164 37338177
GSS50 65326 43053782
GSS51 71507 38514405
GSS52 72842 39272682
GSS53 78759 55275885
GSS54 79583 62734276
GSS55 74220 45780460
GSS56 84423 52718016
GSS57 79195 51487303
GSS58 71163 43367729
GSS59 63626 32797340
GSS6 70440 35413510
GSS60 79300 51211907
GSS61 76916 40755132
GSS62 77410 48720508
GSS63 65409 69912362
GSS64 65112 70044485
GSS65 80732 60900784
GSS66 78499 51502235
GSS67 86693 65544901
GSS68 83144 62398829
GSS69 94515 38475934
GSS7 69562 34942367
GSS70 103988 64736551
GSS71 84901 57297114
GSS72 79159 62377422
GSS73 68541 57426172
GSS74 67634 61669909
GSS75 58971 55461388
GSS76 110011 56316463
GSS77 51714 22863073
GSS8 69966 35810448
GSS9 68097 33824000
HTC1 27554 44223699
HTC2 25839 58503972
HTC3 65066 73891578
HTC4 33686 23811294
HTG1 1330 190557782
HTG10 1230 189302027
HTG11 1413 187314876
HTG12 1004 192041300
HTG13 758 192526815
HTG14 740 192658446
HTG15 763 192446719
HTG16 814 192163463
HTG17 775 192385565
HTG18 1350 186872400
HTG19 1676 182992762
HTG2 2511 188134021
HTG20 945 190970435
HTG21 1278 188287671
HTG22 815 192048166
HTG23 798 192079746
HTG24 994 190794546
HTG25 877 191695574
HTG26 916 191219673
HTG27 799 192075044
HTG28 809 192254809
HTG29 914 191364533
HTG3 2514 187854184
HTG30 909 191634628
HTG31 918 191343319
HTG32 1003 190863519
HTG33 953 191134619
HTG34 926 191417942
HTG35 990 190663524
HTG36 933 191690208
HTG37 877 192131770
HTG38 1056 191024565
HTG39 886 192012075
HTG4 2549 189719538
HTG40 896 191931599
HTG41 884 191740376
HTG42 833 192149477
HTG43 942 191163180
HTG44 964 191414317
HTG45 940 192207932
HTG46 973 191498476
HTG47 983 191447389
HTG48 1111 190967789
HTG49 1192 189454304
HTG5 1292 188316375
HTG50 1254 190211330
HTG51 1200 190432791
HTG52 1097 191658507
HTG53 1170 189781387
HTG54 1087 191650847
HTG55 1253 191349946
HTG56 1237 191542420
HTG57 1006 194034527
HTG58 1297 190935665
HTG59 1210 194275159
HTG6 1288 187785778
HTG60 1047 194039612
HTG61 1024 193476001
HTG62 918 151472672
HTG7 1251 188161830
HTG8 1287 187592659
HTG9 1212 189205653
INV1 10213 172592877
INV2 1270 166147897
INV3 59637 89312876
INV4 59969 86417712
INV5 38116 107056605
INV6 1824 24525023
MAM 49574 61085634
PAT1 220707 69300800
PAT2 178038 90167637
PAT3 144884 84137216
PAT4 107598 114216700
PAT5 146682 86216370
PAT6 125399 74438516
PAT7 104780 59689884
PAT8 126434 46126187
PHG 2338 8744474
PLN1 21273 137350975
PLN2 46003 117488884
PLN3 74965 77221725
PLN4 4880 165060545
PLN5 53193 71135321
PLN6 57725 88624411
PLN7 44392 108874093
PLN8 15023 33899490
PRI1 14384 153588104
PRI10 1392 174330785
PRI11 1276 175262728
PRI12 1506 175030835
PRI13 1585 178902996
PRI14 16097 159152765
PRI15 43389 114483481
PRI16 9562 162510419
PRI17 1611 180116373
PRI18 1757 181588464
PRI19 2283 188133749
PRI2 1410 172026371
PRI20 1369 185684104
PRI21 39664 105718697
PRI22 13926 167624604
PRI23 39105 130213969
PRI24 33046 130245749
PRI25 47857 74792368
PRI3 1258 181737432
PRI4 1285 177918243
PRI5 1142 173747734
PRI6 1215 179319025
PRI7 1203 176752304
PRI8 1321 167525643
PRI9 1224 177564344
ROD1 7088 177032952
ROD2 1072 195032028
ROD3 23246 155866329
ROD4 2259 191568382
ROD5 1184 192485892
ROD6 5962 186086480
ROD7 41498 95004325
ROD8 24349 28757498
STS1 88673 48834345
STS2 83684 34882059
STS3 58676 27019891
SYN 10484 16958300
UNA 621 330976
VRL1 72746 63141819
VRL2 72812 65377857
VRL3 43630 40391951
VRT1 60769 92897451
VRT2 24800 152178209
VRT3 22681 22922042
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 136.0 (chloroplast and mitochon-
drial sequences not included, and Whole Genome Shotgun sequences not included) :
Entries Bases Species
6859992 10035181648 Homo sapiens
4970795 5990618706 Mus musculus
819387 5538846126 Rattus norvegicus
491700 931237063 Danio rerio
350513 689537320 Drosophila melanogaster
220725 648949932 Oryza sativa (japonica cultivar-group)
896468 519905166 Zea mays
567301 469036847 Gallus gallus
518857 400481821 Arabidopsis thaliana
567864 386356083 Brassica oleracea
20919 331338653 Macaca mulatta
499225 294150396 Ciona intestinalis
455779 260696161 Bos taurus
222405 232664948 Caenorhabditis elegans
422871 210449953 Triticum aestivum
166337 198044783 Pan troglodytes
299901 188937000 Xenopus laevis
189208 170811939 Tetraodon nigroviridis
190398 167862132 Medicago truncatula
354095 166704531 Glycine max
2.2.8 Growth of GenBank
The following table lists the number of bases and the number of sequence
records in each release of GenBank, beginning with Release 3 in 1982.
From 1982 to the present, the number of bases in GenBank has doubled
approximately every 14 months.
Release Date Base Pairs Entries
3 Dec 1982 680338 606
14 Nov 1983 2274029 2427
20 May 1984 3002088 3665
24 Sep 1984 3323270 4135
25 Oct 1984 3368765 4175
26 Nov 1984 3689752 4393
32 May 1985 4211931 4954
36 Sep 1985 5204420 5700
40 Feb 1986 5925429 6642
42 May 1986 6765476 7416
44 Aug 1986 8442357 8823
46 Nov 1986 9615371 9978
48 Feb 1987 10961380 10913
50 May 1987 13048473 12534
52 Aug 1987 14855145 14020
53 Sep 1987 15514776 14584
54 Dec 1987 16752872 15465
55 Mar 1988 19156002 17047
56 Jun 1988 20795279 18226
57 Sep 1988 22019698 19044
57.1 Oct 1988 23800000 20579
58 Dec 1988 24690876 21248
59 Mar 1989 26382491 22479
60 Jun 1989 31808784 26317
61 Sep 1989 34762585 28791
62 Dec 1989 37183950 31229
63 Mar 1990 40127752 33377
64 Jun 1990 42495893 35100
65 Sep 1990 49179285 39533
66 Dec 1990 51306092 41057
67 Mar 1991 55169276 43903
68 Jun 1991 65868799 51418
69 Sep 1991 71947426 55627
70 Dec 1991 77337678 58952
71 Mar 1992 83894652 65100
72 Jun 1992 92160761 71280
73 Sep 1992 101008486 78608
74 Dec 1992 120242234 97084
75 Feb 1993 126212259 106684
76 Apr 1993 129968355 111911
77 Jun 1993 138904393 120134
78 Aug 1993 147215633 131328
79 Oct 1993 157152442 143492
80 Dec 1993 163802597 150744
81 Feb 1994 173261500 162946
82 Apr 1994 180589455 169896
83 Jun 1994 191393939 182753
84 Aug 1994 201815802 196703
85 Oct 1994 217102462 215273
86 Dec 1994 230485928 237775
87 Feb 1995 248499214 269478
88 Apr 1995 286094556 352414
89 Jun 1995 318624568 425211
90 Aug 1995 353713490 492483
91 Oct 1995 384939485 555694
92 Dec 1995 425860958 620765
93 Feb 1996 463758833 685693
94 Apr 1996 499127741 744295
95 Jun 1996 551750920 835487
96 Aug 1996 602072354 920588
97 Oct 1996 651972984 1021211
98 Dec 1996 730552938 1114581
99 Feb 1997 786898138 1192505
100 Apr 1997 842864309 1274747
101 Jun 1997 966993087 1491069
102 Aug 1997 1053474516 1610848
103 Oct 1997 1160300687 1765847
104 Dec 1997 1258290513 1891953
105 Feb 1998 1372368913 2042325
106 Apr 1998 1502542306 2209232
107 Jun 1998 1622041465 2355928
108 Aug 1998 1797137713 2532359
109 Oct 1998 2008761784 2837897
110 Dec 1998 2162067871 3043729
111 Apr 1999 2569578208 3525418
112 Jun 1999 2974791993 4028171
113 Aug 1999 3400237391 4610118
114 Oct 1999 3841163011 4864570
115 Dec 1999 4653932745 5354511
116 Feb 2000 5805414935 5691170
117 Apr 2000 7376080723 6215002
118 Jun 2000 8604221980 7077491
119 Aug 2000 9545724824 8214339
120 Oct 2000 10335692655 9102634
121 Dec 2000 11101066288 10106023
122 Feb 2001 11720120326 10896781
123 Apr 2001 12418544023 11545572
124 Jun 2001 12973707065 12243766
125 Aug 2001 13543364296 12813516
126 Oct 2001 14396883064 13602262
127 Dec 2001 15849921438 14976310
128 Feb 2002 17089143893 15465325
129 Apr 2002 19072679701 16769983
130 Jun 2002 20648748345 17471130
131 Aug 2002 22616937182 18197119
132 Oct 2002 26525934656 19808101
133 Dec 2002 28507990166 22318883
134 Feb 2003 29358082791 23035823
135 Apr 2003 31099264455 24027936
136 Jun 2003 32528249295 25592865
3. FILE FORMATS
The flat file examples included in this section, while not always from the
current release, are usually fairly recent. Any differences compared to the
actual records are the result of updates to the entries involved.
3.1 File Header Information
With the exception of the index files, gbcon.seq, and the lists of new,
changed, and deleted accession numbers, each of the 508 files of a GenBank
release begins with the same header, except for the first line, which
contains the file name, and the sixth line, which contains the title of
the file. The first line of the file contains the file name in character
positions 1 to 9 and the full database name (Genetic Sequence Data Bank,
aka 'GenBank') starting in column 22. The brief names of the files in this
release are listed in section 2.2.
The second line contains the date of the current release in the form
`day month year', beginning in position 27. The fourth line contains
the current GenBank release number. The release number appears in
positions 48 to 52 and consists of three numbers separated by a decimal
point. The number to the left of the decimal is the major release
number. The digit to the right of the decimal indicates the version of
the major release; it is zero for the first version. The sixth line
contains a title for the file. The eighth line lists the number of
entries (loci), number of bases (or base pairs), and number of reports
of sequences (equal to number of entries in this case). These numbers are
right-justified at fixed positions. The number of entries appears in
positions 1 to 8, the number of bases in positions 16 to 26, and the
number of reports in positions 40 to 47. The third, fifth, seventh, and
ninth lines are blank.
1 10 20 30 40 50 60 70 79
---------+---------+---------+---------+---------+---------+---------+---------
GBBCT1.SEQ Genetic Sequence Data Bank
15 April 2003
NCBI-GenBank Flat File Release 136.0
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/projects/collab/FT/index.html
Any discrepancy between the abbreviated feature table description
of these release notes and the complete documentation on the Web
should be resolved in favor of the version at the above URL.
The Feature Table specification is also available as a printed
document: `The DDBJ/EMBL/GenBank Feature Table: Definition'. Contact
GenBank at the address shown on the first page of these Release Notes
if you would like a copy.
The feature table contains information about genes and gene products,
as well as regions of biological significance reported in the
sequence. The feature table contains information on regions of the
sequence that code for proteins and RNA molecules. It also enumerates
differences between different reports of the same sequence, and
provides cross-references to other data collections, as described in
more detail below.
The first line of the feature table is a header that includes the
keyword `FEATURES' and the column header `Location/Qualifier.' Each
feature consists of a descriptor line containing a feature key and a
location (see sections below for details). If the location does not
fit on this line, a continuation line may follow. If further
information about the feature is required, one or more lines
containing feature qualifiers may follow the descriptor line.
The feature key begins in column 6 and may be no more than 15
characters in length. The location begins in column 22. Feature
qualifiers begin on subsequent lines at column 22. Location,
qualifier, and continuation lines may extend from column 22 to 80.
Feature tables are required, due to the mandatory presence of the
source feature. The sections below provide a brief introduction to
the feature table format.
3.4.12.1 Feature Key Names
The first column of the feature descriptor line contains the feature
key. It starts at column 6 and can continue to column 20. The list of
valid feature keys is shown below.
Remember, the most definitive documentation for the feature table can
be found at:
http://www.ncbi.nlm.nih.gov/projects/collab/FT/index.html
allele Obsolete; see variation feature key
attenuator Sequence related to transcription termination
C_region Span of the C immunological feature
CAAT_signal `CAAT box' in eukaryotic promoters
CDS Sequence coding for amino acids in protein (includes
stop codon)
conflict Independent sequence determinations differ
D-loop Displacement loop
D_segment Span of the D immunological feature
enhancer Cis-acting enhancer of promoter function
exon Region that codes for part of spliced mRNA
gene Region that defines a functional gene, possibly
including upstream (promotor, enhancer, etc)
and downstream control elements, and for which
a name has been assigned.
GC_signal `GC box' in eukaryotic promoters
iDNA Intervening DNA eliminated by recombination
intron Transcribed region excised by mRNA splicing
J_region Span of the J immunological feature
LTR Long terminal repeat
mat_peptide Mature peptide coding region (does not include stop codon)
misc_binding Miscellaneous binding site
misc_difference Miscellaneous difference feature
misc_feature Region of biological significance that cannot be described
by any other feature
misc_recomb Miscellaneous recombination feature
misc_RNA Miscellaneous transcript feature not defined by other RNA keys
misc_signal Miscellaneous signal
misc_structure Miscellaneous DNA or RNA structure
modified_base The indicated base is a modified nucleotide
mRNA Messenger RNA
mutation Obsolete: see variation feature key
N_region Span of the N immunological feature
old_sequence Presented sequence revises a previous version
polyA_signal Signal for cleavage & polyadenylation
polyA_site Site at which polyadenine is added to mRNA
precursor_RNA Any RNA species that is not yet the mature RNA product
prim_transcript Primary (unprocessed) transcript
primer Primer binding region used with PCR
primer_bind Non-covalent primer binding site
promoter A region involved in transcription initiation
protein_bind Non-covalent protein binding site on DNA or RNA
RBS Ribosome binding site
rep_origin Replication origin for duplex DNA
repeat_region Sequence containing repeated subsequences
repeat_unit One repeated unit of a repeat_region
rRNA Ribosomal RNA
S_region Span of the S immunological feature
satellite Satellite repeated sequence
scRNA Small cytoplasmic RNA
sig_peptide Signal peptide coding region
snRNA Small nuclear RNA
source Biological source of the sequence data represented by
a GenBank record. Mandatory feature, one or more per record.
For organisms that have been incorporated within the
NCBI taxonomy database, an associated /db_xref="taxon:NNNN"
qualifier will be present (where NNNNN is the numeric
identifier assigned to the organism within the NCBI taxonomy
database).
stem_loop Hair-pin loop structure in DNA or RNA
STS Sequence Tagged Site; operationally unique sequence that
identifies the combination of primer spans used in a PCR assay
TATA_signal `TATA box' in eukaryotic promoters
terminator Sequence causing transcription termination
transit_peptide Transit peptide coding region
transposon Transposable element (TN)
tRNA Transfer RNA
unsure Authors are unsure about the sequence in this region
V_region Span of the V immunological feature
variation A related population contains stable mutation
- (hyphen) Placeholder
-10_signal `Pribnow box' in prokaryotic promoters
-35_signal `-35 box' in prokaryotic promoters
3'clip 3'-most region of a precursor transcript removed in processing
3'UTR 3' untranslated region (trailer)
5'clip 5'-most region of a precursor transcript removed in processing
5'UTR 5' untranslated region (leader)
3.4.12.2 Feature Location
The second column of the feature descriptor line designates the
location of the feature in the sequence. The location descriptor
begins at position 22. Several conventions are used to indicate
sequence location.
Base numbers in location descriptors refer to numbering in the entry,
which is not necessarily the same as the numbering scheme used in the
published report. The first base in the presented sequence is numbered
base 1. Sequences are presented in the 5 to 3 direction.
Location descriptors can be one of the following:
1. A single base;
2. A contiguous span of bases;
3. A site between two bases;
4. A single base chosen from a range of bases;
5. A single base chosen from among two or more specified bases;
6. A joining of sequence spans;
7. A reference to an entry other than the one to which the feature
belongs (i.e., a remote entry), followed by a location descriptor
referring to the remote sequence;
A site between two residues, such as an endonuclease cleavage site, is
indicated by listing the two bases separated by a carat (e.g., 23^24).
A single residue chosen from a range of residues is indicated by the
number of the first and last bases in the range separated by a single
period (e.g., 23.79). The symbols < and > indicate that the end point
of the range is beyond the specified base number.
A contiguous span of bases is indicated by the number of the first and
last bases in the range separated by two periods (e.g., 23..79). The
symbols < and > indicate that the end point of the range is beyond the
specified base number. Starting and ending positions can be indicated
by base number or by one of the operators described below.
Operators are prefixes that specify what must be done to the indicated
sequence to locate the feature. The following are the operators
available, along with their most common format and a description.
complement (location): The feature is complementary to the location
indicated. Complementary strands are read 5 to 3.
join (location, location, .. location): The indicated elements should
be placed end to end to form one contiguous sequence.
order (location, location, .. location): The elements are found in the
specified order in the 5 to 3 direction, but nothing is implied about
the rationality of joining them.
3.4.12.3 Feature Qualifiers
Qualifiers provide additional information about features. They take
the form of a slash (/) followed by a qualifier name and, if
applicable, an equal sign (=) and a qualifier value. Feature
qualifiers begin at column 22.
Qualifiers convey many types of information. Their values can,
therefore, take several forms:
1. Free text;
2. Controlled vocabulary or enumerated values;
3. Citations or reference numbers;
4. Sequences;
5. Feature labels.
Text qualifier values must be enclosed in double quotation marks. The
text can consist of any printable characters (ASCII values 32-126
decimal). If the text string includes double quotation marks, each set
must be `escaped' by placing a double quotation mark in front of it
(e.g., /note="This is an example of ""escaped"" quotation marks").
Some qualifiers require values selected from a limited set of choices.
For example, the `/direction' qualifier has only three values `left,'
`right,' or `both.' These are called controlled vocabulary qualifier
values. Controlled qualifier values are not case sensitive; they can
be entered in any combination of upper- and lowercase without changing
their meaning.
Citation or published reference numbers for the entry should be
enclosed in square brackets ([]) to distinguish them from other
numbers.
A literal sequence of bases (e.g., "atgcatt") should be enclosed in
quotation marks. Literal sequences are distinguished from free text by
context. Qualifiers that take free text as their values do not take
literal sequences, and vice versa.
The `/label=' qualifier takes a feature label as its qualifier.
Although feature labels are optional, they allow unambiguous
references to the feature. The feature label identifies a feature
within an entry; when combined with the accession number and the name
of the data bank from which it came, it is a unique tag for that
feature. Feature labels must be unique within an entry, but can be the
same as a feature label in another entry. Feature labels are not case
sensitive; they can be entered in any combination of upper-and
lowercase without changing their meaning.
The following is a partial list of feature qualifiers.
/anticodon Location of the anticodon of tRNA and the amino acid
for which it codes
/bound_moiety Moiety bound
/citation Reference to a citation providing the claim of or
evidence for a feature
/codon Specifies a codon that is different from any found in the
reference genetic code
/codon_start Indicates the first base of the first complete codon
in a CDS (as 1 or 2 or 3)
/cons_splice Identifies intron splice sites that do not conform to
the 5'-GT... AG-3' splice site consensus
/db_xref A database cross-reference; pointer to related information
in another database. A description of all cross-references
can be found at:
http://www.ncbi.nlm.nih.gov/collab/db_xref.html
/direction Direction of DNA replication
/EC_number Enzyme Commission number for the enzyme product of the
sequence
/evidence Value indicating the nature of supporting evidence
/frequency Frequency of the occurrence of a feature
/function Function attributed to a sequence
/gene Symbol of the gene corresponding to a sequence region (usable
with all features)
/label A label used to permanently identify a feature
/map Map position of the feature in free-format text
/mod_base Abbreviation for a modified nucleotide base
/note Any comment or additional information
/number A number indicating the order of genetic elements
(e.g., exons or introns) in the 5 to 3 direction
/organism Name of the organism that is the source of the
sequence data in the record.
/partial Differentiates between complete regions and partial ones
/phenotype Phenotype conferred by the feature
/product Name of a product encoded by a coding region (CDS)
feature
/pseudo Indicates that this feature is a non-functional
version of the element named by the feature key
/rpt_family Type of repeated sequence; Alu or Kpn, for example
/rpt_type Organization of repeated sequence
/rpt_unit Identity of repeat unit that constitutes a repeat_region
/standard_name Accepted standard name for this feature
/transl_except Translational exception: single codon, the translation
of which does not conform to the reference genetic code
/translation Amino acid translation of a coding region
/type Name of a strain if different from that in the SOURCE field
/usedin Indicates that feature is used in a compound feature
in another entry
3.4.12.4 Cross-Reference Information
One type of information in the feature table lists cross-references to
the annual compilation of transfer RNA sequences in Nucleic Acids
Research, which has kindly been sent to us on CD-ROM by Dr. Sprinzl.
Each tRNA entry of the feature table contains a /note= qualifier that
includes a reference such as `(NAR: 1234)' to identify code 1234 in
the NAR compilation. When such a cross-reference appears in an entry
that contains a gene coding for a transfer RNA molecule, it refers to
the code in the tRNA gene compilation. Similar cross-references in
entries containing mature transfer RNA sequences refer to the
companion compilation of tRNA sequences published by D.H. Gauss and M.
Sprinzl in Nucleic Acids Research.
3.4.12.5 Feature Table Examples
In the first example a number of key names, feature locations, and
qualifiers are illustrated, taken from different sequences. The first
table entry is a coding region consisting of a simple span of bases
and including a /gene qualifier. In the second table entry, an NAR
cross-reference is given (see the previous section for a discussion of
these cross-references). The third and fourth table entries use the
symbols `<`and `>' to indicate that the beginning or end of the
feature is beyond the range of the presented sequence. In the fifth
table entry, the symbol `^' indicates that the feature is between
bases.
1 10 20 30 40 50 60 70 79
---------+---------+---------+---------+---------+---------+---------+---------
CDS 5..1261
/product="alpha-1-antitrypsin precursor"
/map="14q32.1"
/gene="PI"
tRNA 1..87
/note="Leu-tRNA-CAA (NAR: 1057)"
/anticodon=(pos:35..37,aa:Leu)
mRNA 1..>66
/note="alpha-1-acid glycoprotein mRNA"
transposon <1..267
/note="insertion element IS5"
misc_recomb 105^106
/note="B.subtilis DNA end/IS5 DNA start"
conflict 258
/replace="t"
/citation=[2]
---------+---------+---------+---------+---------+---------+---------+---------
1 10 20 30 40 50 60 70 79
Example 10. Feature Table Entries
The next example shows the representation for a CDS that spans more
than one entry.
1 10 20 30 40 50 60 70 79
---------+---------+---------+---------+---------+---------+---------+---------
LOCUS HUMPGAMM1 3688 bp ds-DNA PRI 15-OCT-1990
DEFINITION Human phosphoglycerate mutase (muscle specific isozyme) (PGAM-M)
gene, 5' end.
ACCESSION M55673 M25818 M27095
KEYWORDS phosphoglycerate mutase.
SEGMENT 1 of 2
.
.
.
FEATURES Location/Qualifiers
CAAT_signal 1751..1755
/gene="PGAM-M"
TATA_signal 1791..1799
/gene="PGAM-M"
exon 1820..2274
/number=1
/EC_number="5.4.2.1"
/gene="PGAM-M"
intron 2275..2377
/number=1
/gene="PGAM2"
exon 2378..2558
/number=2
/gene="PGAM-M"
.
.
.
//
LOCUS HUMPGAMM2 677 bp ds-DNA PRI 15-OCT-1990
DEFINITION Human phosphoglycerate mutase (muscle specific isozyme) (PGAM-M),
exon 3.
ACCESSION M55674 M25818 M27096
KEYWORDS phosphoglycerate mutase.
SEGMENT 2 of 2
.
.
.
FEATURES Location/Qualifiers
exon 255..457
/number=3
/gene="PGAM-M"
intron order(M55673:2559..>3688,<1..254)
/number=2
/gene="PGAM-M"
mRNA join(M55673:1820..2274,M55673:2378..2558,255..457)
/gene="PGAM-M"
CDS join(M55673:1861..2274,M55673:2378..2558,255..421)
/note="muscle-specific isozyme"
/gene="PGAM2"
/product="phosphoglycerate mutase"
/codon_start=1
/translation="MATHRLVMVRHGESTWNQENRFCGWFDAELSEKGTEEAKRGAKA
IKDAKMEFDICYTSVLKRAIRTLWAILDGTDQMWLPVVRTWRLNERHYGGLTGLNKAE
TAAKHGEEQVKIWRRSFDIPPPPMDEKHPYYNSISKERRYAGLKPGELPTCESLKDTI
ARALPFWNEEIVPQIKAGKRVLIAAHGNSLRGIVKHLEGMSDQAIMELNLPTGIPIVY
ELNKELKPTKPMQFLGDEETVRKAMEAVAAQGKAK"
.
.
.
//
---------+---------+---------+---------+---------+---------+---------+---------
1 10 20 30 40 50 60 70 79
Example 11. Joining Sequences
3.4.13 ORIGIN Format
The ORIGIN record may be left blank, may appear as `Unreported.' or
may give a local pointer to the sequence start, usually involving an
experimentally determined restriction cleavage site or the genetic
locus (if available). The ORIGIN record ends in a period if it
contains data, but does not include the period if the record is left
empty (in contrast to the KEYWORDS field which contains a period
rather than being left blank).
3.4.14 SEQUENCE Format
The nucleotide sequence for an entry is found in the records following
the ORIGIN record. The sequence is reported in the 5 to 3 direction.
There are sixty bases per record, listed in groups of ten bases
followed by a blank, starting at position 11 of each record. The
number of the first nucleotide in the record is given in columns 4 to
9 (right justified) of the record.
4. ALTERNATE RELEASES
NCBI is supplying sequence data in the GenBank flat file format to
maintain compatibility with existing software which require that
particular format. Although we have made every effort to ensure
that these data are presented in the traditional flat file format,
if you encounter any problems in using these data with software which
is based upon the flat file format, please contact us at:
[email protected]
The flat file is just one of many possible report formats that can be
generated from the richer representation supported by the ASN.1 form of the
data. Developers of new software tools should consider using the ASN.1 form
directly to take advantage of those features. Documentation and a Software
Developer's Toolkit for ASN.1 are available through NCBI. You may call NCBI
at (301)496-2475, or subscribe to a developers' electronic newsgroup by
sending your name, address, affiliation, and e-mail address to:
[email protected]
The Software Developer's Toolkit and PostScript documentation for UNIX,
VMS, Ultrix, AIX, MacOS, DOS, and Microsoft Windows systems is available
in a compressed UNIX tar file by anonymous ftp from 'ftp.ncbi.nih.gov',
in the toolbox/ncbi_tools directory. The file is 'ncbi.tar.Z'.
5. KNOWN PROBLEMS OF THE GENBANK DATABASE
5.1 Incorrect Gene Symbols in Entries and Index
The /gene qualifier for many GenBank entries contains values other than the
official gene symbol, such as the product or the standard name of the gene. The
gene symbol index (gbgen.idx) is created from the data in the /gene qualifier
and therefore may contain data other than official gene symbols.
6. GENBANK ADMINISTRATION
The National Center for Biotechnology Information (NCBI), National Library
of Medicine, National Institutes of Health, is responsible for the production
and distribution of the NIH GenBank Sequence Database. NCBI distributes
GenBank sequence data by anonymous FTP, e-mail servers and other
network services. For more information, you may contact NCBI at the
e-mail address: [email protected] or by phone: 301-496-2475.
6.1 Registered Trademark Notice
GenBank (R) is a registered trademark of the U.S. Department of Health
and Human Services for the Genetic Sequence Data Bank.
6.2 Citing GenBank
If you have used GenBank in your research, we would appreciate it if
you would include a reference to GenBank in all publications related
to that research.
When citing data in GenBank, it is appropriate to give the sequence
name, primary accession number, and the publication in which the
sequence first appeared. If the data are unpublished, we urge you to
contact the group which submitted the data to GenBank to see if there
is a recent publication or if they have determined any revisions or
extensions of the data.
It is also appropriate to list a reference for GenBank itself. The
following publication, which describes the GenBank database, should
be cited:
Benson D.A., Karsch-Mizrachi I., Lipman D.J., Ostell J., Rapp B.A.,
Wheeler D.L. GenBank. Nucl. Acids Res. 28(1):15-18 (2000)
The following statement is an example of how you may cite GenBank
data. It cites the sequence, its primary accession number, the group
who determined the sequence, and GenBank. The numbers in parentheses
refer to the GenBank citation above and to the REFERENCE in the
GenBank sequence entry.
`We scanned the GenBank (1) database for sequence similarities and
found one sequence (2), GenBank accession number J01016, which showed
significant similarity...'
(1) Benson, D.A. et al. Nucl. Acids Res. 28(1):15-18 (2000)
(2) Nellen, W. and Gallwitz, D. J. Mol. Biol. 159, 1-18 (1982)
6.3 GenBank Distribution Formats and Media
Complete flat file releases of the GenBank database are available via
NCBI's anonymous ftp server:
ftp://ftp.ncbi.nih.gov
Each release is cumulative, incorporating all previous GenBank data.
No retrieval software is provided. GenBank distribution via CD-ROM
ceased as of GenBank Release 106.0 (April, 1998).
Mirrors of the GenBank FTP site at the NCBI are available from the
San Diego Supercomputer Center and the University of Indiana:
ftp://genbank.sdsc.edu/pub
ftp://bio-mirror.net/biomirror/genbank/
6.4 Other Methods of Accessing GenBank Data
Entrez is a molecular biology database system that presents an integrated
view of DNA and protein sequence data, 3D structure data, complete genomes,
and associated MEDLINE entries. The system is produced by the National
Center for Biotechnology Information (NCBI), and is available only via
the Internet (using the Web-Entrez and Network-Entrez applications).
Accessing Entrez is easy: if you have a World Wide Web browser, such as
Netscape or Internet-Explorer, simply point your browser to:
http://www.ncbi.nlm.nih.gov/
The Web version of Entrez has all the capabilities of the network version,
but with the visual style of the World Wide Web. If you prefer the "look and
feel" of Network-Entrez, you may download Network-Entrez from the NCBI's
FTP server:
ftp://ftp.ncbi.nih.gov/
Versions are available for PC/Windows, Macintosh and several Unix variants.
For information about Network-Entrez, Web-Entrez or any other NCBI
services, you may contact NCBI by e-mail at [email protected] or by
phone at 301-496-2475.
6.5 Request for Corrections and Comments
We welcome your suggestions for improvements to GenBank. We are
especially interested to learn of errors or inconsistencies in the
data. BankIt or Sequin can be used to submit revisions to previous
submissions. In addition, suggestions and corrections can be sent by
electronic mail to: [email protected]. Please be certain to
indicate the GenBank release number (e.g., Release 136.0) 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, William Klimke, Pierre Ledoux,
Richard McVeigh, Ilene Mizrachi, DeAnne Olsen Cravaritis,
Chris O'Sullivan, Leigh Riley, Gert Roosen, MJ Rosovitz, Susan Schafer,
Suh-suh Wang, 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,
Karl Sirotkin, Vladimir Soussov, Elena Starchenko, Hanzhen Sun,
Tatiana Tatusov, Carolyn Tolstoshev, Jane Weisemann, Eugene Yaschenko
Database Administration
Ron Chen, Slava Khotomliansky, Tony Stearman
User Support
Medha Bhagwat, Peter Cooper, Susan Dombrowski, Andrei Gabrielian
Renata Geer, Scott McGinnis, Donna Messersmith, Rana Morris, Vyvy Pham,
Monica Romiti, Eric Sayers, Tao Tao, David Wheeler
Project Direction
David Lipman
Acknowledgments -
Contractor support for GenBank production and distribution has been
provided by Management Systems Designers, Inc., ComputerCraft Corporation,
and The KEVRIC Company, Inc.
6.7 Disclaimer
The United States Government makes no representations or warranties
regarding the content or accuracy of the information. The United States
Government also makes no representations or warranties of merchantability
or fitness for a particular purpose or that the use of the sequences will
not infringe any patent, copyright, trademark, or other rights. The
United States Government accepts no responsibility for any consequence
of the receipt or use of the information.
For additional information about GenBank releases, please contact
NCBI by e-mail at [email protected], by phone at (301) 496-2475,
or by mail at:
GenBank
National Library of Medicine
Bldg. 38A Rm. 8N-809
8600 Rockville Pike
Bethesda, MD 20894
FAX: (301) 480-9241
