Release Notes For GenBank Release 132
GBREL.TXT Genetic Sequence Data Bank
October 15 2002
NCBI-GenBank Flat File Release 132.0
Distribution Release Notes
19808101 loci, 26525934656 bases, from 19808101 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 132.0
1.2 Cutoff Date
1.3 Important Changes in Release 132.0
1.4 Upcoming Changes
1.5 Request for Direct Submission of Sequence Data
1.6 Organization of This Document
2. ORGANIZATION OF DATA FILES
2.1 Overview
2.2 Files
2.2.1 File Descriptions
2.2.5 File Sizes
2.2.6 Per-Division Statistics
2.2.7 Selected Per-Organism Statistics
2.2.8 Growth of GenBank
3. FILE FORMATS
3.1 File Header Information
3.2 Directory Files
3.2.1 Short Directory File
3.3 Index Files
3.3.1 Accession Number Index File
3.3.2 Keyword Phrase Index File
3.3.3 Author Name Index File
3.3.4 Journal Citation Index File
3.3.5 Gene Name Index
3.4 Sequence Entry Files
3.4.1 File Organization
3.4.2 Entry Organization
3.4.3 Sample Sequence Data File
3.4.4 LOCUS Format
3.4.5 DEFINITION Format
3.4.5.1 DEFINITION Format for NLM Entries
3.4.6 ACCESSION Format
3.4.7 VERSION Format
3.4.8 KEYWORDS Format
3.4.9 SEGMENT Format
3.4.10 SOURCE Format
3.4.11 REFERENCE Format
3.4.12 FEATURES Format
3.4.12.1 Feature Key Names
3.4.12.2 Feature Location
3.4.12.3 Feature Qualifiers
3.4.12.4 Cross-Reference Information
3.4.12.5 Feature Table Examples
3.4.13 ORIGIN Format
3.4.14 SEQUENCE Format
4. ALTERNATE RELEASES
5. KNOWN PROBLEMS OF THE GENBANK DATABASE
5.1 Incorrect Gene Symbols in Entries and Index
6. GENBANK ADMINISTRATION
6.1 Registered Trademark Notice
6.2 Citing GenBank
6.3 GenBank Distribution Formats and Media
6.4 Other Methods of Accessing GenBank Data
6.5 Request for Corrections and Comments
6.6 Credits and Acknowledgments
6.7 Disclaimer
==========================================================================
1. INTRODUCTION
1.1 Release 132.0
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 132.0 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, 132.0, incorporates data available to the collaborating
databases as of October 29, 2002. For more recent data, users are advised to:
o Download the GenBank Update files by anonymous FTP to 'ftp.ncbi.nih.gov':
ftp://ftp.ncbi.nih.gov/ncbi-asn1 (ASN.1 format)
ftp://ftp.ncbi.nih.gov/genbank (flatfile format)
Mirrors of the GenBank FTP site at the NCBI are available from the San Diego
Supercomputer Center and the University of Indiana:
ftp://genbank.sdsc.edu/pub
ftp://bio-mirror.net/biomirror/genbank/
Some users who experience slow FTP transfers of large files (entire releases,
the GenBank Cumulative Update, etc) might realize an improvement in transfer
rates from these alternate sites when traffic at the NCBI is high.
o Use the interactive Network-Entrez or Web-Entrez applications to query
the 'Entrez: Nucleotides' database (see Section 6.4 of this document).
1.3 Important Changes in Release 132.0
1.3.1 Organizational changes
Due to database growth, the BCT division is now being split into 6 pieces.
Due to database growth, the EST division is now being split into 190 pieces.
Due to database growth, the GSS division is now being split into 59 pieces.
Due to database growth, the HTC division has been newly split into two pieces,
gbhtc1.seq and gbhtc2.seq .
Due to database growth, the HTG division is now being split into 56 pieces.
Due to database growth, the PAT division is now being split into 6 pieces.
Due to database growth, the PRI division is now being split into 22 pieces.
Due to database growth, the ROD division is now being split into 5 pieces.
1.3.2 Full-Length-Insert cDNA Problem; Supplemental Release File
Due to a change in the way sequences associated with full-length-insert cDNA
sequencing projects are handled at the NCBI, 19,345 records were inadvertently
excluded from the normal divisional GenBank sequence data files. Given the delays
caused by the database-wide SOURCE/ORGANISM format change (see Section 1.3.4),
we have elected to make these records available via a supplemental datafile,
since the alternatives would have resulted in further delays:
gbsup.seq
The records that this 'SUP' data file contains will be distributed among the
normal divisions (INV, PLN, etc) for GenBank Release 133.0 . Our apologies for
any inconvenience that the presence of this additional file might cause.
1.3.3 Minor REFERENCE format change
A small number of records in GenBank have more than 99 literature references
and/or database submission references. This leads to a formatting problem for
the REFERENCE line:
LOCUS SV4CG 5243 bp DNA circular VRL 14-DEC-2000
DEFINITION Simian virus 40 complete genome.
ACCESSION J02400 J02402 J02403 J02406 J02407 J02408 J02409 J02410 J04139
M24874 M24914 M28728 V01380
VERSION J02400.1 GI:965480
....
REFERENCE 100(sites)
AUTHORS Mertz,J.E., Murphy,A. and Barkan,A.
TITLE Mutants deleted in the agnogene of simian virus 40 define a new
complementation group
JOURNAL J. Virol. 45 (1), 36-46 (1983)
MEDLINE 83112203
PUBMED 6296443
REFERENCE 101(bases 1 to 129; 5228 to 5243)
AUTHORS Byrne,B.J., Davis,M.S., Yamaguchi,J., Bergsma,D.J. and
Subramanian,K.N.
TITLE Definition of the simian virus 40 early promoter region and
demonstration of a host range bias in the enhancement effect of the
simian virus 40 72-base-pair repeat
JOURNAL Proc. Natl. Acad. Sci. U.S.A. 80 (3), 721-725 (1983)
MEDLINE 83144002
PUBMED 6298771
Note the lack of a space between the REFERENCE number and the basepair span
(or 'sites' designation).
Since the REFERENCE format is not column-specific beyond column 13 (see
Section 3.4.11), we have addressed this problem by simply adding a space after
any REFERENCE number greater than 99. Those who might parse baserange (or sites)
information from REFERENCE lines based on a column position should modify their
software to tokenize on whitespace characters instead.
1.3.4 Change to the SOURCE and ORGANISM format
Starting with this October 2002 GenBank Release 132.0, a new more flexible SOURCE
format has been adopted, allowing for the display of several types of secondary
names (common names, acronyms, synonyms, anamorphs for the fungi) which can be
derived either from the taxonomy database *or* from the source feature annotation
provided by the submitter.
In addition, the optional organelle prefix has moved from the ORGANISM line
(in the old format) to the SOURCE line in the new format. The ORGANISM line
now contains only the unadorned organism name, the name by which a sequence
entry is indexed in the taxonomy database.
--- Previous GenBank format ---
SOURCE [organism name] OR [common name]
ORGANISM [organelle prefix] organism name
--- New GenBank format ---
SOURCE [organelle prefix] organism name ([optional second name])
ORGANISM organism name
The optional second name can be one of the following (ordered by precedence) -
'synonym' from the source feature organism modifiers (submitter-supplied)
'acronym' from the source feature organism modifiers (submitter-supplied)
'anamorph' from the source feature organism modifiers (submitter-supplied)
'common' from the source feature organism modifiers (submitter-supplied)
'genbank synonym' from the taxonomy database
'genbank acronmym' from the taxonomy database
'genbank anamorph' from the taxonomy database
'genbank common name' from the taxonomy database
The first set allows us to customize the flatfiles of particular entries,
the last allows us to add useful & informative information from the
taxonomy database, with a more reasonable presentation than the previous
format allowed.
The 'anamorph' names appear within parentheses prefixed with (anamorph: ---).
The 'common name', 'acronym' and 'synonym' fields are parenthesized without
a prefix (see examples below).
The SOURCE line organelle prefix corresponds to the most detailed portion
of the string value for the /organelle qualifier of the source feature. This
allows us to annotate everything with the correct general terms, yet prominently
display the familiar 'Chloroplast' & 'Kinetoplast' :
organelle qualifer SOURCE organelle prefix
----------------- -----------------------
"plastid" plastid
"mitochondrion" mitochondrion
"nucleomorph" nucleomorph
"mitochondrion: kinetoplast" kinetoplast
"plastid: chloroplast" chloroplast
"plastid: apicoplast" apicoplast
"plastid: chromoplast" chromoplast
"plastid: cyanelle" cyanelle
"plastid: leucoplast" leucoplast
"plastid: protoplast" protoplast
=======================================================
====== Examples of the new format ======
=======================================================
In all of the examples below, the source feature qualifiers given in the first
part of the example automatically generate the SOURCE & ORGANISM lines shown:
------------------------
/organism="Sus scrofa"
SOURCE Sus scrofa (pig)
ORGANISM Sus scrofa
'pig' is the genbank common name from the GenBank taxonomy database.
------------------------
/organism="Sus scrofa"
/note="common: Japanese wild boar"
SOURCE Sus scrofa (Japanese wild boar)
ORGANISM Sus scrofa
The common name from the source feature (submittor-suppllied) for
the entry overrides the common name from the GenBank taxonomy database
with the new SOURCE format.
------------------------
/organism="Takifugu rubripes"
SOURCE Takifugu rubripes (Fugu rubripes)
ORGANISM Takifugu rubripes
'genbank synonym' from the taxonomy database is displayed on the SOURCE
line.
------------------------
/organism="Takifugu rubripes"
/note="common: Sydney's pufferfish"
SOURCE Takifugu rubripes (Sydney's pufferfish)
ORGANISM Takifugu rubripes
Any of the customizing fields from the entry itself take precedence
over the default values from the taxonomy database.
------------------------
/organism="Cauliflower mosaic virus"
SOURCE Cauliflower mosaic virus (CaMV)
ORGANISM Cauliflower mosaic virus
If there is a single acronym listed in the taxonomy database,
it will appear on the SOURCE line.
------------------------
'genbank anamorph' (from the taxonomy database)
/organism="Emericella nidulans"
SOURCE Emericella nidulans (anamorph: Aspergillus nidulans)
ORGANISM Emericella nidulans
The 'anamorph' nametype is prefixed with "anamorph:" on the SOURCE line
to distinguish it from a taxonomic synonym.
------------------------
/organism="Mytilus californicus"
/organelle="mitochondrion"
SOURCE mitochondrion Mytilus californicus (California mussel)
ORGANISM Mytilus californicus
Organelle prefix moved to SOURCE; common name from the GenBank taxonomy
database has been added to SOURCE .
1.3.5 GSS File Header Problem
GSS sequences at GenBank are maintained in one of two different systems,
depending on their origin. One recent change to release processing involves
the parallelization of the dumps from those systems. Because the second dump
(for example) has no prior knowledge of exactly how many GSS files will be
dumped from the first, it doesn't know how to number it's own output files.
There is thus a discrepancy between the filenames and file headers of nine
GSS flatfiles in Release 132.0. Consider the gbgss51.seq file:
GBGSS1.SEQ Genetic Sequence Data Bank
October 15 2002
NCBI-GenBank Flat File Release 132.0
GSS Sequences (Part 1)
88406 loci, 66834201 bases, from 88406 reported sequences
Here, the filename and part number in the header is "1", though the file
has been renamed as "51" based on the files dumped from the other system.
We will work to resolve this discrepancy in future releases, but the
priority is certainly much lower than many other tasks.
1.4 Upcoming Changes
1.4.1 * * Cumulative GenBank Update Products To Be Discontinued * *
As of GenBank Release 134.0 in February of 2002, the cumulative
GenBank Update (GBCU) products will be discontinued:
ftp://ftp.ncbi.nih.gov/ncbi-asn1/daily/gbcu.aso.gz
ftp://ftp.ncbi.nih.gov/genbank/daily/gbcu.flat.gz
ftp://ftp.ncbi.nih.gov/genbank/daily/gbcu.fsa_nt.gz
ftp://ftp.ncbi.nih.gov/genbank/daily/gbcu.gnp.gz
ftp://ftp.ncbi.nih.gov/genbank/daily/gbcu.qscore.gz
ftp://ftp.ncbi.nih.gov/genbank/daily/gpcu.fsa.gz
In the eight weeks between typical GenBank Releases, it is not uncommon
for GBCU products to approach 20% of the total database size. The flatfile
version, for example, has reached sizes in excess of 15 GB in recent weeks.
From a user perspective, repeatedly obtaining and processing such a
large update product makes inefficient use of both bandwidth and local
resources, compared to the much smaller incremental GbUpdate products.
And in order to reliably generate the GBCU in the face of such explosive
growth, NCBI would have to invest significant resources to increase the
performance of a large body of software.
Given these factors, plus the questionable value of an "update" product,
generated daily, which will soon approach 20GB in size, we have decided
that the GBCU should be discontinued. We will analyze FTP logs and
proactively contact the larger centers which utilize the GBCU, to suggest
alternate processing strategies.
If large numbers of users are unable to switch to processing incremental
updates by February 2002, there is a possibility that the date for
discontinuing the GBCU might be pushed back to April.
We will keep users informed of the timetable for this important change
via these release notes and the GenBank newsgroup. And of course, we
welcome discussions of this change via the newsgroup.
1.4.2 New SET Data File For The ASN.1 Representation
Some phylogenetic and mutational studies involve sequences from more
than one of the 'taxonomic' divisions of GenBank. For example, a phylogenetic
study might involve sequences obtained from human (PRI) and non-primate
mammalian (MAM) sources.
Such studies, often with associated sequence alignments, are maintained
and edited as a single unit in the underlying data representation (ASN.1)
utilized by the NCBI.
When generating GenBank flatfiles from such studies, the component
sequences are processed in such a way that they are individually directed
to an appropriate divisional file. For example, the human sequences to a
PRI division file, the other mammalian sequences to the MAM division file.
In the past, we have mimicked this behavior for the ASN.1 version of
GenBank releases by splitting the studies into their components, and
splicing them into an appropriate divisional ASN.1 file (eg, gbpri1.aso
and gbmam.aso) .
This practice has clear disadvantages: the components of the studies
really should *not* be separated; and the post-processing of these special
studies adds considerable overhead to release processing.
Starting with GenBank Release 133.0 in December of 2002, we will cease
this practice and introduce a new ASN.1 data file for such multi-divisional
studies at ftp://ftp.ncbi.nih.gov/ncbi-asn1 . The new file will be :
gbset.aso
1.4.3 Reduction In The Number Of ASN.1 Data Files
The sizes of many of the files for the ASN.1 version of GenBank releases
(see ftp://ftp.ncbi.nih.gov/ncbi-asn1 ) is well below the 250 MB utilized
for the GenBank flatfile version. For example, the PRI division ASN.1 files
are about 140 MB apiece, and the HTG division files are about 190 MB apiece.
This is due to the fact that the ASN.1 representation was originally
used to create the flatfile version, on a file-by-file basis, during release
generation. Since the ASN.1 version is more compact than the flatfile version,
the ASN.1 file sizes had to be less than 250 MB to yield 250 MB flatfiles.
Now that the ASN.1 and flatfile versions are created independently, the
sizes of the ASN.1 files can be increased without consequences for the
flatfiles.
Starting with the December 2002 Release 133.0, the file size limit for all
ASN.1 files will be increased to 250MB, and as a result, the total number of
ASN.1 files will be significantly reduced.
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 390 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. gbjou.idx - Index of the entries according to journal citation.
19. gbgen.idx - Index of the entries according to gene names.
20. gbsec.idx - Index of the entries according to secondary accession number.
21. gbpri1.seq - Primate sequence entries, part 1.
22. gbpri2.seq - Primate sequence entries, part 2.
23. gbpri3.seq - Primate sequence entries, part 3.
24. gbpri4.seq - Primate sequence entries, part 4.
25. gbpri5.seq - Primate sequence entries, part 5.
26. gbpri6.seq - Primate sequence entries, part 6.
27. gbpri7.seq - Primate sequence entries, part 7.
28. gbpri8.seq - Primate sequence entries, part 8.
29. gbpri9.seq - Primate sequence entries, part 9.
30. gbpri10.seq - Primate sequence entries, part 10.
31. gbpri11.seq - Primate sequence entries, part 11.
32. gbpri12.seq - Primate sequence entries, part 12.
33. gbpri13.seq - Primate sequence entries, part 13.
34. gbpri14.seq - Primate sequence entries, part 14.
35. gbpri15.seq - Primate sequence entries, part 15.
36. gbpri16.seq - Primate sequence entries, part 16.
37. gbpri17.seq - Primate sequence entries, part 17.
38. gbpri18.seq - Primate sequence entries, part 18.
39. gbpri19.seq - Primate sequence entries, part 19.
40. gbpri20.seq - Primate sequence entries, part 20.
41. gbpri21.seq - Primate sequence entries, part 21.
42. gbpri22.seq - Primate sequence entries, part 22.
43. gbpri23.seq - Primate sequence entries, part 23.
44. gbrod1.seq - Rodent sequence entries, part 1.
45. gbrod2.seq - Rodent sequence entries, part 2.
46. gbrod3.seq - Rodent sequence entries, part 3.
47. gbrod4.seq - Rodent sequence entries, part 4.
48. gbrod5.seq - Rodent sequence entries, part 5.
49. gbmam.seq - Other mammalian sequence entries.
50. gbvrt1.seq - Other vertebrate sequence entries, part 1.
51. gbvrt2.seq - Other vertebrate sequence entries, part 2.
52. gbinv1.seq - Invertebrate sequence entries, part 1.
53. gbinv2.seq - Invertebrate sequence entries, part 2.
54. gbinv3.seq - Invertebrate sequence entries, part 3.
55. gbinv4.seq - Invertebrate sequence entries, part 4.
56. gbinv5.seq - Invertebrate sequence entries, part 5.
57. gbpln1.seq - Plant sequence entries (including fungi and algae), part 1.
58. gbpln2.seq - Plant sequence entries (including fungi and algae), part 2.
59. gbpln3.seq - Plant sequence entries (including fungi and algae), part 3.
60. gbpln4.seq - Plant sequence entries (including fungi and algae), part 4.
61. gbpln5.seq - Plant sequence entries (including fungi and algae), part 5.
62. gbpln6.seq - Plant sequence entries (including fungi and algae), part 6.
63. gbbct1.seq - Bacterial sequence entries, part 1.
64. gbbct2.seq - Bacterial sequence entries, part 2.
65. gbbct3.seq - Bacterial sequence entries, part 3.
66. gbbct4.seq - Bacterial sequence entries, part 4.
67. gbbct5.seq - Bacterial sequence entries, part 5.
68. gbbct6.seq - Bacterial sequence entries, part 6.
69. gbvrl1.seq - Viral sequence entries, part 1.
70. gbvrl2.seq - Viral sequence entries, part 2.
71. gbvrl3.seq - Viral sequence entries, part 3.
72. gbphg.seq - Phage sequence entries.
73. gbsyn.seq - Synthetic and chimeric sequence entries.
74. gbuna.seq - Unannotated sequence entries.
75. gbest1.seq - EST (expressed sequence tag) sequence entries, part 1.
76. gbest2.seq - EST (expressed sequence tag) sequence entries, part 2.
77. gbest3.seq - EST (expressed sequence tag) sequence entries, part 3.
78. gbest4.seq - EST (expressed sequence tag) sequence entries, part 4.
79. gbest5.seq - EST (expressed sequence tag) sequence entries, part 5.
80. gbest6.seq - EST (expressed sequence tag) sequence entries, part 6.
81. gbest7.seq - EST (expressed sequence tag) sequence entries, part 7.
82. gbest8.seq - EST (expressed sequence tag) sequence entries, part 8.
83. gbest9.seq - EST (expressed sequence tag) sequence entries, part 9.
84. gbest10.seq - EST (expressed sequence tag) sequence entries, part 10.
85. gbest11.seq - EST (expressed sequence tag) sequence entries, part 11.
86. gbest12.seq - EST (expressed sequence tag) sequence entries, part 12.
87. gbest13.seq - EST (expressed sequence tag) sequence entries, part 13.
88. gbest14.seq - EST (expressed sequence tag) sequence entries, part 14.
89. gbest15.seq - EST (expressed sequence tag) sequence entries, part 15.
90. gbest16.seq - EST (expressed sequence tag) sequence entries, part 16.
91. gbest17.seq - EST (expressed sequence tag) sequence entries, part 17.
92. gbest18.seq - EST (expressed sequence tag) sequence entries, part 18.
93. gbest19.seq - EST (expressed sequence tag) sequence entries, part 19.
94. gbest20.seq - EST (expressed sequence tag) sequence entries, part 20.
95. gbest21.seq - EST (expressed sequence tag) sequence entries, part 21.
96. gbest22.seq - EST (expressed sequence tag) sequence entries, part 22.
97. gbest23.seq - EST (expressed sequence tag) sequence entries, part 23.
98. gbest24.seq - EST (expressed sequence tag) sequence entries, part 24.
99. gbest25.seq - EST (expressed sequence tag) sequence entries, part 25.
100. gbest26.seq - EST (expressed sequence tag) sequence entries, part 26.
101. gbest27.seq - EST (expressed sequence tag) sequence entries, part 27.
102. gbest28.seq - EST (expressed sequence tag) sequence entries, part 28.
103. gbest29.seq - EST (expressed sequence tag) sequence entries, part 29.
104. gbest30.seq - EST (expressed sequence tag) sequence entries, part 30.
105. gbest31.seq - EST (expressed sequence tag) sequence entries, part 31.
106. gbest32.seq - EST (expressed sequence tag) sequence entries, part 32.
107. gbest33.seq - EST (expressed sequence tag) sequence entries, part 33.
108. gbest34.seq - EST (expressed sequence tag) sequence entries, part 34.
109. gbest35.seq - EST (expressed sequence tag) sequence entries, part 35.
110. gbest36.seq - EST (expressed sequence tag) sequence entries, part 36.
111. gbest37.seq - EST (expressed sequence tag) sequence entries, part 37.
112. gbest38.seq - EST (expressed sequence tag) sequence entries, part 38.
113. gbest39.seq - EST (expressed sequence tag) sequence entries, part 39.
114. gbest40.seq - EST (expressed sequence tag) sequence entries, part 40.
115. gbest41.seq - EST (expressed sequence tag) sequence entries, part 41.
116. gbest42.seq - EST (expressed sequence tag) sequence entries, part 42.
117. gbest43.seq - EST (expressed sequence tag) sequence entries, part 43.
118. gbest44.seq - EST (expressed sequence tag) sequence entries, part 44.
119. gbest45.seq - EST (expressed sequence tag) sequence entries, part 45.
120. gbest46.seq - EST (expressed sequence tag) sequence entries, part 46.
121. gbest47.seq - EST (expressed sequence tag) sequence entries, part 47.
122. gbest48.seq - EST (expressed sequence tag) sequence entries, part 48.
123. gbest49.seq - EST (expressed sequence tag) sequence entries, part 49.
124. gbest50.seq - EST (expressed sequence tag) sequence entries, part 50.
125. gbest51.seq - EST (expressed sequence tag) sequence entries, part 51.
126. gbest52.seq - EST (expressed sequence tag) sequence entries, part 52.
127. gbest53.seq - EST (expressed sequence tag) sequence entries, part 53.
128. gbest54.seq - EST (expressed sequence tag) sequence entries, part 54.
129. gbest55.seq - EST (expressed sequence tag) sequence entries, part 55.
130. gbest56.seq - EST (expressed sequence tag) sequence entries, part 56.
131. gbest57.seq - EST (expressed sequence tag) sequence entries, part 57.
132. gbest58.seq - EST (expressed sequence tag) sequence entries, part 58.
133. gbest59.seq - EST (expressed sequence tag) sequence entries, part 59.
134. gbest60.seq - EST (expressed sequence tag) sequence entries, part 60.
135. gbest61.seq - EST (expressed sequence tag) sequence entries, part 61.
136. gbest62.seq - EST (expressed sequence tag) sequence entries, part 62.
137. gbest63.seq - EST (expressed sequence tag) sequence entries, part 63.
138. gbest64.seq - EST (expressed sequence tag) sequence entries, part 64.
139. gbest65.seq - EST (expressed sequence tag) sequence entries, part 65.
140. gbest66.seq - EST (expressed sequence tag) sequence entries, part 66.
141. gbest67.seq - EST (expressed sequence tag) sequence entries, part 67.
142. gbest68.seq - EST (expressed sequence tag) sequence entries, part 68.
143. gbest69.seq - EST (expressed sequence tag) sequence entries, part 69.
144. gbest70.seq - EST (expressed sequence tag) sequence entries, part 70.
145. gbest71.seq - EST (expressed sequence tag) sequence entries, part 71.
146. gbest72.seq - EST (expressed sequence tag) sequence entries, part 72.
147. gbest73.seq - EST (expressed sequence tag) sequence entries, part 73.
148. gbest74.seq - EST (expressed sequence tag) sequence entries, part 74.
149. gbest75.seq - EST (expressed sequence tag) sequence entries, part 75.
150. gbest76.seq - EST (expressed sequence tag) sequence entries, part 76.
151. gbest77.seq - EST (expressed sequence tag) sequence entries, part 77.
152. gbest78.seq - EST (expressed sequence tag) sequence entries, part 78.
153. gbest79.seq - EST (expressed sequence tag) sequence entries, part 79.
154. gbest80.seq - EST (expressed sequence tag) sequence entries, part 80.
155. gbest81.seq - EST (expressed sequence tag) sequence entries, part 81.
156. gbest82.seq - EST (expressed sequence tag) sequence entries, part 82.
157. gbest83.seq - EST (expressed sequence tag) sequence entries, part 83.
158. gbest84.seq - EST (expressed sequence tag) sequence entries, part 84.
159. gbest85.seq - EST (expressed sequence tag) sequence entries, part 85.
160. gbest86.seq - EST (expressed sequence tag) sequence entries, part 86.
161. gbest87.seq - EST (expressed sequence tag) sequence entries, part 87.
162. gbest88.seq - EST (expressed sequence tag) sequence entries, part 88.
163. gbest89.seq - EST (expressed sequence tag) sequence entries, part 89
164. gbest90.seq - EST (expressed sequence tag) sequence entries, part 90.
165. gbest91.seq - EST (expressed sequence tag) sequence entries, part 91.
166. gbest92.seq - EST (expressed sequence tag) sequence entries, part 92.
167. gbest93.seq - EST (expressed sequence tag) sequence entries, part 93.
168. gbest94.seq - EST (expressed sequence tag) sequence entries, part 94.
169. gbest95.seq - EST (expressed sequence tag) sequence entries, part 95.
170. gbest96.seq - EST (expressed sequence tag) sequence entries, part 96.
171. gbest97.seq - EST (expressed sequence tag) sequence entries, part 97.
172. gbest98.seq - EST (expressed sequence tag) sequence entries, part 98.
173. gbest99.seq - EST (expressed sequence tag) sequence entries, part 99.
174. gbest100.seq - EST (expressed sequence tag) sequence entries, part 100.
175. gbest101.seq - EST (expressed sequence tag) sequence entries, part 101.
176. gbest102.seq - EST (expressed sequence tag) sequence entries, part 102.
177. gbest103.seq - EST (expressed sequence tag) sequence entries, part 103.
178. gbest104.seq - EST (expressed sequence tag) sequence entries, part 104.
179. gbest105.seq - EST (expressed sequence tag) sequence entries, part 105.
180. gbest106.seq - EST (expressed sequence tag) sequence entries, part 106.
181. gbest107.seq - EST (expressed sequence tag) sequence entries, part 107.
182. gbest108.seq - EST (expressed sequence tag) sequence entries, part 108.
183. gbest109.seq - EST (expressed sequence tag) sequence entries, part 109.
184. gbest110.seq - EST (expressed sequence tag) sequence entries, part 110.
185. gbest111.seq - EST (expressed sequence tag) sequence entries, part 111.
186. gbest112.seq - EST (expressed sequence tag) sequence entries, part 112.
187. gbest113.seq - EST (expressed sequence tag) sequence entries, part 113.
188. gbest114.seq - EST (expressed sequence tag) sequence entries, part 114.
189. gbest115.seq - EST (expressed sequence tag) sequence entries, part 115.
190. gbest116.seq - EST (expressed sequence tag) sequence entries, part 116.
191. gbest117.seq - EST (expressed sequence tag) sequence entries, part 117.
192. gbest118.seq - EST (expressed sequence tag) sequence entries, part 118.
193. gbest119.seq - EST (expressed sequence tag) sequence entries, part 119.
194. gbest120.seq - EST (expressed sequence tag) sequence entries, part 120.
195. gbest121.seq - EST (expressed sequence tag) sequence entries, part 121.
196. gbest122.seq - EST (expressed sequence tag) sequence entries, part 122.
197. gbest123.seq - EST (expressed sequence tag) sequence entries, part 123.
198. gbest124.seq - EST (expressed sequence tag) sequence entries, part 124.
199. gbest125.seq - EST (expressed sequence tag) sequence entries, part 125.
200. gbest126.seq - EST (expressed sequence tag) sequence entries, part 126.
201. gbest127.seq - EST (expressed sequence tag) sequence entries, part 127.
202. gbest128.seq - EST (expressed sequence tag) sequence entries, part 128.
203. gbest129.seq - EST (expressed sequence tag) sequence entries, part 129.
204. gbest130.seq - EST (expressed sequence tag) sequence entries, part 130.
205. gbest131.seq - EST (expressed sequence tag) sequence entries, part 131.
206. gbest132.seq - EST (expressed sequence tag) sequence entries, part 132.
207. gbest133.seq - EST (expressed sequence tag) sequence entries, part 133.
208. gbest134.seq - EST (expressed sequence tag) sequence entries, part 134.
209. gbest135.seq - EST (expressed sequence tag) sequence entries, part 135.
210. gbest136.seq - EST (expressed sequence tag) sequence entries, part 136.
211. gbest137.seq - EST (expressed sequence tag) sequence entries, part 137.
212. gbest138.seq - EST (expressed sequence tag) sequence entries, part 138.
213. gbest139.seq - EST (expressed sequence tag) sequence entries, part 139.
214. gbest140.seq - EST (expressed sequence tag) sequence entries, part 140.
215. gbest141.seq - EST (expressed sequence tag) sequence entries, part 141.
216. gbest142.seq - EST (expressed sequence tag) sequence entries, part 142.
217. gbest143.seq - EST (expressed sequence tag) sequence entries, part 143.
218. gbest144.seq - EST (expressed sequence tag) sequence entries, part 144.
219. gbest145.seq - EST (expressed sequence tag) sequence entries, part 145.
220. gbest146.seq - EST (expressed sequence tag) sequence entries, part 146.
221. gbest147.seq - EST (expressed sequence tag) sequence entries, part 147.
222. gbest148.seq - EST (expressed sequence tag) sequence entries, part 148.
223. gbest149.seq - EST (expressed sequence tag) sequence entries, part 149.
224. gbest150.seq - EST (expressed sequence tag) sequence entries, part 150.
225. gbest151.seq - EST (expressed sequence tag) sequence entries, part 151.
226. gbest152.seq - EST (expressed sequence tag) sequence entries, part 152.
227. gbest153.seq - EST (expressed sequence tag) sequence entries, part 153.
228. gbest154.seq - EST (expressed sequence tag) sequence entries, part 154.
229. gbest155.seq - EST (expressed sequence tag) sequence entries, part 155.
230. gbest156.seq - EST (expressed sequence tag) sequence entries, part 156.
231. gbest157.seq - EST (expressed sequence tag) sequence entries, part 157.
232. gbest158.seq - EST (expressed sequence tag) sequence entries, part 158.
233. gbest159.seq - EST (expressed sequence tag) sequence entries, part 159.
234. gbest160.seq - EST (expressed sequence tag) sequence entries, part 160.
235. gbest161.seq - EST (expressed sequence tag) sequence entries, part 161.
236. gbest162.seq - EST (expressed sequence tag) sequence entries, part 162.
237. gbest163.seq - EST (expressed sequence tag) sequence entries, part 163.
238. gbest164.seq - EST (expressed sequence tag) sequence entries, part 164.
239. gbest165.seq - EST (expressed sequence tag) sequence entries, part 165.
240. gbest166.seq - EST (expressed sequence tag) sequence entries, part 166.
241. gbest167.seq - EST (expressed sequence tag) sequence entries, part 167.
242. gbest168.seq - EST (expressed sequence tag) sequence entries, part 168.
243. gbest169.seq - EST (expressed sequence tag) sequence entries, part 169.
244. gbest170.seq - EST (expressed sequence tag) sequence entries, part 170.
245. gbest171.seq - EST (expressed sequence tag) sequence entries, part 171.
246. gbest172.seq - EST (expressed sequence tag) sequence entries, part 172.
247. gbest173.seq - EST (expressed sequence tag) sequence entries, part 173.
248. gbest174.seq - EST (expressed sequence tag) sequence entries, part 174.
249. gbest175.seq - EST (expressed sequence tag) sequence entries, part 175.
250. gbest176.seq - EST (expressed sequence tag) sequence entries, part 176.
251. gbest177.seq - EST (expressed sequence tag) sequence entries, part 177.
252. gbest178.seq - EST (expressed sequence tag) sequence entries, part 178.
253. gbest179.seq - EST (expressed sequence tag) sequence entries, part 179.
254. gbest180.seq - EST (expressed sequence tag) sequence entries, part 180.
255. gbest181.seq - EST (expressed sequence tag) sequence entries, part 181.
256. gbest182.seq - EST (expressed sequence tag) sequence entries, part 182.
257. gbest183.seq - EST (expressed sequence tag) sequence entries, part 183.
258. gbest184.seq - EST (expressed sequence tag) sequence entries, part 184.
259. gbest185.seq - EST (expressed sequence tag) sequence entries, part 185.
260. gbest186.seq - EST (expressed sequence tag) sequence entries, part 186.
261. gbest187.seq - EST (expressed sequence tag) sequence entries, part 187.
262. gbest188.seq - EST (expressed sequence tag) sequence entries, part 188.
263. gbest189.seq - EST (expressed sequence tag) sequence entries, part 189.
264. gbest190.seq - EST (expressed sequence tag) sequence entries, part 190.
265. gbpat1.seq - Patent sequence entries, part 1.
266. gbpat2.seq - Patent sequence entries, part 2.
267. gbpat3.seq - Patent sequence entries, part 3.
268. gbpat4.seq - Patent sequence entries, part 4.
269. gbpat5.seq - Patent sequence entries, part 5.
270. gbpat6.seq - Patent sequence entries, part 6.
271. gbsts1.seq - STS (sequence tagged site) sequence entries, part 1.
272. gbsts2.seq - STS (sequence tagged site) sequence entries, part 2.
273. gbgss1.seq - GSS (genome survey sequence) sequence entries, part 1.
274. gbgss2.seq - GSS (genome survey sequence) sequence entries, part 2.
275. gbgss3.seq - GSS (genome survey sequence) sequence entries, part 3.
276. gbgss4.seq - GSS (genome survey sequence) sequence entries, part 4.
277. gbgss5.seq - GSS (genome survey sequence) sequence entries, part 5.
278. gbgss6.seq - GSS (genome survey sequence) sequence entries, part 6.
279. gbgss7.seq - GSS (genome survey sequence) sequence entries, part 7.
280. gbgss8.seq - GSS (genome survey sequence) sequence entries, part 8.
281. gbgss9.seq - GSS (genome survey sequence) sequence entries, part 9.
282. gbgss10.seq - GSS (genome survey sequence) sequence entries, part 10.
283. gbgss11.seq - GSS (genome survey sequence) sequence entries, part 11.
284. gbgss12.seq - GSS (genome survey sequence) sequence entries, part 12.
285. gbgss13.seq - GSS (genome survey sequence) sequence entries, part 13.
286. gbgss14.seq - GSS (genome survey sequence) sequence entries, part 14.
287. gbgss15.seq - GSS (genome survey sequence) sequence entries, part 15.
288. gbgss16.seq - GSS (genome survey sequence) sequence entries, part 16.
289. gbgss17.seq - GSS (genome survey sequence) sequence entries, part 17.
290. gbgss18.seq - GSS (genome survey sequence) sequence entries, part 18.
291. gbgss19.seq - GSS (genome survey sequence) sequence entries, part 19.
292. gbgss20.seq - GSS (genome survey sequence) sequence entries, part 20.
293. gbgss21.seq - GSS (genome survey sequence) sequence entries, part 21.
294. gbgss22.seq - GSS (genome survey sequence) sequence entries, part 22.
295. gbgss23.seq - GSS (genome survey sequence) sequence entries, part 23.
296. gbgss24.seq - GSS (genome survey sequence) sequence entries, part 24.
297. gbgss25.seq - GSS (genome survey sequence) sequence entries, part 25.
298. gbgss26.seq - GSS (genome survey sequence) sequence entries, part 26.
299. gbgss27.seq - GSS (genome survey sequence) sequence entries, part 27.
300. gbgss28.seq - GSS (genome survey sequence) sequence entries, part 28.
301. gbgss29.seq - GSS (genome survey sequence) sequence entries, part 29.
302. gbgss30.seq - GSS (genome survey sequence) sequence entries, part 30.
303. gbgss31.seq - GSS (genome survey sequence) sequence entries, part 31.
304. gbgss32.seq - GSS (genome survey sequence) sequence entries, part 32.
305. gbgss33.seq - GSS (genome survey sequence) sequence entries, part 33.
306. gbgss34.seq - GSS (genome survey sequence) sequence entries, part 34.
307. gbgss35.seq - GSS (genome survey sequence) sequence entries, part 35.
308. gbgss36.seq - GSS (genome survey sequence) sequence entries, part 36.
309. gbgss37.seq - GSS (genome survey sequence) sequence entries, part 37.
310. gbgss38.seq - GSS (genome survey sequence) sequence entries, part 38.
311. gbgss39.seq - GSS (genome survey sequence) sequence entries, part 39.
312. gbgss40.seq - GSS (genome survey sequence) sequence entries, part 40.
313. gbgss41.seq - GSS (genome survey sequence) sequence entries, part 41.
314. gbgss42.seq - GSS (genome survey sequence) sequence entries, part 42.
315. gbgss43.seq - GSS (genome survey sequence) sequence entries, part 43.
316. gbgss44.seq - GSS (genome survey sequence) sequence entries, part 44.
317. gbgss45.seq - GSS (genome survey sequence) sequence entries, part 45.
318. gbgss46.seq - GSS (genome survey sequence) sequence entries, part 46.
319. gbgss47.seq - GSS (genome survey sequence) sequence entries, part 47.
320. gbgss48.seq - GSS (genome survey sequence) sequence entries, part 48.
321. gbgss49.seq - GSS (genome survey sequence) sequence entries, part 49.
322. gbgss50.seq - GSS (genome survey sequence) sequence entries, part 50.
323. gbgss51.seq - GSS (genome survey sequence) sequence entries, part 51.
324. gbgss52.seq - GSS (genome survey sequence) sequence entries, part 52.
325. gbgss53.seq - GSS (genome survey sequence) sequence entries, part 53.
326. gbgss54.seq - GSS (genome survey sequence) sequence entries, part 54.
327. gbgss55.seq - GSS (genome survey sequence) sequence entries, part 55.
328. gbgss56.seq - GSS (genome survey sequence) sequence entries, part 56.
329. gbgss57.seq - GSS (genome survey sequence) sequence entries, part 57.
330. gbgss58.seq - GSS (genome survey sequence) sequence entries, part 58.
331. gbgss59.seq - GSS (genome survey sequence) sequence entries, part 59.
332. gbhtg1.seq - HTGS (high throughput genomic sequencing) sequence entries, part 1.
333. gbhtg2.seq - HTGS (high throughput genomic sequencing) sequence entries, part 2.
334. gbhtg3.seq - HTGS (high throughput genomic sequencing) sequence entries, part 3.
335. gbhtg4.seq - HTGS (high throughput genomic sequencing) sequence entries, part 4.
336. gbhtg5.seq - HTGS (high throughput genomic sequencing) sequence entries, part 5.
337. gbhtg6.seq - HTGS (high throughput genomic sequencing) sequence entries, part 6.
338. gbhtg7.seq - HTGS (high throughput genomic sequencing) sequence entries, part 7.
339. gbhtg8.seq - HTGS (high throughput genomic sequencing) sequence entries, part 8.
340. gbhtg9.seq - HTGS (high throughput genomic sequencing) sequence entries, part 9.
341. gbhtg10.seq - HTGS (high throughput genomic sequencing) sequence entries, part 10.
342. gbhtg11.seq - HTGS (high throughput genomic sequencing) sequence entries, part 11.
343. gbhtg12.seq - HTGS (high throughput genomic sequencing) sequence entries, part 12.
344. gbhtg13.seq - HTGS (high throughput genomic sequencing) sequence entries, part 13.
345. gbhtg14.seq - HTGS (high throughput genomic sequencing) sequence entries, part 14.
346. gbhtg15.seq - HTGS (high throughput genomic sequencing) sequence entries, part 15.
347. gbhtg16.seq - HTGS (high throughput genomic sequencing) sequence entries, part 16.
348. gbhtg17.seq - HTGS (high throughput genomic sequencing) sequence entries, part 17.
349. gbhtg18.seq - HTGS (high throughput genomic sequencing) sequence entries, part 18.
350. gbhtg19.seq - HTGS (high throughput genomic sequencing) sequence entries, part 19.
351. gbhtg20.seq - HTGS (high throughput genomic sequencing) sequence entries, part 20.
352. gbhtg21.seq - HTGS (high throughput genomic sequencing) sequence entries, part 21.
353. gbhtg22.seq - HTGS (high throughput genomic sequencing) sequence entries, part 22.
354. gbhtg23.seq - HTGS (high throughput genomic sequencing) sequence entries, part 23.
355. gbhtg24.seq - HTGS (high throughput genomic sequencing) sequence entries, part 24.
356. gbhtg25.seq - HTGS (high throughput genomic sequencing) sequence entries, part 25.
357. gbhtg26.seq - HTGS (high throughput genomic sequencing) sequence entries, part 26.
358. gbhtg27.seq - HTGS (high throughput genomic sequencing) sequence entries, part 27.
359. gbhtg28.seq - HTGS (high throughput genomic sequencing) sequence entries, part 28.
360. gbhtg29.seq - HTGS (high throughput genomic sequencing) sequence entries, part 29.
361. gbhtg30.seq - HTGS (high throughput genomic sequencing) sequence entries, part 30.
362. gbhtg31.seq - HTGS (high throughput genomic sequencing) sequence entries, part 31.
363. gbhtg32.seq - HTGS (high throughput genomic sequencing) sequence entries, part 32.
364. gbhtg33.seq - HTGS (high throughput genomic sequencing) sequence entries, part 33.
365. gbhtg34.seq - HTGS (high throughput genomic sequencing) sequence entries, part 34.
366. gbhtg35.seq - HTGS (high throughput genomic sequencing) sequence entries, part 35.
367. gbhtg36.seq - HTGS (high throughput genomic sequencing) sequence entries, part 36.
368. gbhtg37.seq - HTGS (high throughput genomic sequencing) sequence entries, part 37.
369. gbhtg38.seq - HTGS (high throughput genomic sequencing) sequence entries, part 38.
370. gbhtg39.seq - HTGS (high throughput genomic sequencing) sequence entries, part 39.
371. gbhtg40.seq - HTGS (high throughput genomic sequencing) sequence entries, part 40.
372. gbhtg41.seq - HTGS (high throughput genomic sequencing) sequence entries, part 41.
373. gbhtg42.seq - HTGS (high throughput genomic sequencing) sequence entries, part 42.
374. gbhtg43.seq - HTGS (high throughput genomic sequencing) sequence entries, part 43.
375. gbhtg44.seq - HTGS (high throughput genomic sequencing) sequence entries, part 44.
376. gbhtg45.seq - HTGS (high throughput genomic sequencing) sequence entries, part 45.
377. gbhtg46.seq - HTGS (high throughput genomic sequencing) sequence entries, part 46.
378. gbhtg47.seq - HTGS (high throughput genomic sequencing) sequence entries, part 47.
379. gbhtg48.seq - HTGS (high throughput genomic sequencing) sequence entries, part 48.
380. gbhtg49.seq - HTGS (high throughput genomic sequencing) sequence entries, part 49.
381. gbhtg50.seq - HTGS (high throughput genomic sequencing) sequence entries, part 50.
382. gbhtg51.seq - HTGS (high throughput genomic sequencing) sequence entries, part 51.
383. gbhtg52.seq - HTGS (high throughput genomic sequencing) sequence entries, part 52.
384. gbhtg53.seq - HTGS (high throughput genomic sequencing) sequence entries, part 53.
385. gbhtg54.seq - HTGS (high throughput genomic sequencing) sequence entries, part 54.
386. gbhtg55.seq - HTGS (high throughput genomic sequencing) sequence entries, part 55.
387. gbhtg56.seq - HTGS (high throughput genomic sequencing) sequence entries, part 56.
388. gbhtc1.seq - HTC (high throughput cDNA sequencing) entries, part 1.
389. gbhtc2.seq - HTC (high throughput cDNA sequencing) entries, part 2.
390. gbsup.seq - SUP (supplemental) sequence entries.
Three Supplemental files provide the accession numbers of GenBank entries
that are new, updated, or deleted since the previous release:
a. gbchg.txt - Entries updated since the previous release.
b. gbdel.txt - Entries deleted since the previous release.
c. gbnew.txt - Entries new since the previous release.
An experimental file called gbcon.seq provides an alternative representation
for complex sequences, such as "segmented sets" and complete-genomes that have
been split into pieces. The GenBank README describes the experimental CON
division of GenBank in more detail:
ftp://ftp.ncbi.nih.gov/genbank/README.genbank
2.2.5 File Sizes
Uncompressed, the Release 132.0 flatfiles require roughly 83.35 GB (sequence
files only) or 92.75 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
645512925 gbacc.idx
501494165 gbaut1.idx
501231525 gbaut10.idx
502667939 gbaut11.idx
517403629 gbaut12.idx
114827556 gbaut13.idx
517086612 gbaut2.idx
500670890 gbaut3.idx
504884972 gbaut4.idx
503065951 gbaut5.idx
500239435 gbaut6.idx
503893200 gbaut7.idx
500015731 gbaut8.idx
508525483 gbaut9.idx
250004951 gbbct1.seq
250002161 gbbct2.seq
250111872 gbbct3.seq
250169393 gbbct4.seq
250000946 gbbct5.seq
34966912 gbbct6.seq
4603740 gbchg.txt
14844 gbdel.txt
230688218 gbest1.seq
230688602 gbest10.seq
230689230 gbest100.seq
230688635 gbest101.seq
230688568 gbest102.seq
230688440 gbest103.seq
230687530 gbest104.seq
230689738 gbest105.seq
230688061 gbest106.seq
230688215 gbest107.seq
230687928 gbest108.seq
230689617 gbest109.seq
230687774 gbest11.seq
230689560 gbest110.seq
230687491 gbest111.seq
230689150 gbest112.seq
230687990 gbest113.seq
230688041 gbest114.seq
230689051 gbest115.seq
230690142 gbest116.seq
230689835 gbest117.seq
230688087 gbest118.seq
230689804 gbest119.seq
230689555 gbest12.seq
230688210 gbest120.seq
230687936 gbest121.seq
227613411 gbest122.seq
230688449 gbest123.seq
230690254 gbest124.seq
230690199 gbest125.seq
230689545 gbest126.seq
230687817 gbest127.seq
230687971 gbest128.seq
230690600 gbest129.seq
230689130 gbest13.seq
230687747 gbest130.seq
230688227 gbest131.seq
230690475 gbest132.seq
230688706 gbest133.seq
230688133 gbest134.seq
230689382 gbest135.seq
230687811 gbest136.seq
230688925 gbest137.seq
230688858 gbest138.seq
230689779 gbest139.seq
230688494 gbest14.seq
230688557 gbest140.seq
230688475 gbest141.seq
230689178 gbest142.seq
230688020 gbest143.seq
230688280 gbest144.seq
230690670 gbest145.seq
230689012 gbest146.seq
230691564 gbest147.seq
230687440 gbest148.seq
230689653 gbest149.seq
230689715 gbest15.seq
230689220 gbest150.seq
230691355 gbest151.seq
230688105 gbest152.seq
230689983 gbest153.seq
230688429 gbest154.seq
230687462 gbest155.seq
230690279 gbest156.seq
230689086 gbest157.seq
230687550 gbest158.seq
230689399 gbest159.seq
230688349 gbest16.seq
230689659 gbest160.seq
230690573 gbest161.seq
227882753 gbest162.seq
230688510 gbest163.seq
230687733 gbest164.seq
230687518 gbest165.seq
230689317 gbest166.seq
230690349 gbest167.seq
230687980 gbest168.seq
230688552 gbest169.seq
230689938 gbest17.seq
230688961 gbest170.seq
230691384 gbest171.seq
230690075 gbest172.seq
230688577 gbest173.seq
230688152 gbest174.seq
230688290 gbest175.seq
230687563 gbest176.seq
230689844 gbest177.seq
230690308 gbest178.seq
230688414 gbest179.seq
230688493 gbest18.seq
230688911 gbest180.seq
230688648 gbest181.seq
230687673 gbest182.seq
230687572 gbest183.seq
230689159 gbest184.seq
230688572 gbest185.seq
230689385 gbest186.seq
230688688 gbest187.seq
230689008 gbest188.seq
230689660 gbest189.seq
230688745 gbest19.seq
91130223 gbest190.seq
230690082 gbest2.seq
230687922 gbest20.seq
230689713 gbest21.seq
230688535 gbest22.seq
230688590 gbest23.seq
230689071 gbest24.seq
230688417 gbest25.seq
230689813 gbest26.seq
230688139 gbest27.seq
230688883 gbest28.seq
230689480 gbest29.seq
230687525 gbest3.seq
230689393 gbest30.seq
230687683 gbest31.seq
230689169 gbest32.seq
230688915 gbest33.seq
230688188 gbest34.seq
230690930 gbest35.seq
210439229 gbest36.seq
209894425 gbest37.seq
214883998 gbest38.seq
215239658 gbest39.seq
230688624 gbest4.seq
216600706 gbest40.seq
216628256 gbest41.seq
217046092 gbest42.seq
230688372 gbest43.seq
230687961 gbest44.seq
224057426 gbest45.seq
230689225 gbest46.seq
230687981 gbest47.seq
230689246 gbest48.seq
230688915 gbest49.seq
164606477 gbest5.seq
230689448 gbest50.seq
230687693 gbest51.seq
230689982 gbest52.seq
230688140 gbest53.seq
230689684 gbest54.seq
230688314 gbest55.seq
230690044 gbest56.seq
230688257 gbest57.seq
230687820 gbest58.seq
230689089 gbest59.seq
180528300 gbest6.seq
230687752 gbest60.seq
223566375 gbest61.seq
209593312 gbest62.seq
209350579 gbest63.seq
209078395 gbest64.seq
209502036 gbest65.seq
210760280 gbest66.seq
209587376 gbest67.seq
208596759 gbest68.seq
210111572 gbest69.seq
230689955 gbest7.seq
210332933 gbest70.seq
205619458 gbest71.seq
207624882 gbest72.seq
207702448 gbest73.seq
209168774 gbest74.seq
218607107 gbest75.seq
230691600 gbest76.seq
230691392 gbest77.seq
230689908 gbest78.seq
224806293 gbest79.seq
230687814 gbest8.seq
215871585 gbest80.seq
220956722 gbest81.seq
230688088 gbest82.seq
230688119 gbest83.seq
230689510 gbest84.seq
230688204 gbest85.seq
230690530 gbest86.seq
230687693 gbest87.seq
230689572 gbest88.seq
230687775 gbest89.seq
230687682 gbest9.seq
230688326 gbest90.seq
230689248 gbest91.seq
230687711 gbest92.seq
230690383 gbest93.seq
230687717 gbest94.seq
230687637 gbest95.seq
230687921 gbest96.seq
230687769 gbest97.seq
230689642 gbest98.seq
230688607 gbest99.seq
26119625 gbgen.idx
209717803 gbgss1.seq
209716015 gbgss10.seq
209716228 gbgss11.seq
209717923 gbgss12.seq
209716672 gbgss13.seq
209718213 gbgss14.seq
209717767 gbgss15.seq
209716722 gbgss16.seq
209717107 gbgss17.seq
209718400 gbgss18.seq
209719313 gbgss19.seq
209717267 gbgss2.seq
209718244 gbgss20.seq
209719378 gbgss21.seq
209717365 gbgss22.seq
209716185 gbgss23.seq
209719893 gbgss24.seq
209717640 gbgss25.seq
209716700 gbgss26.seq
209717557 gbgss27.seq
209718409 gbgss28.seq
209716700 gbgss29.seq
209717479 gbgss3.seq
209716708 gbgss30.seq
209717216 gbgss31.seq
209719216 gbgss32.seq
209716666 gbgss33.seq
209717639 gbgss34.seq
209718364 gbgss35.seq
209715922 gbgss36.seq
209718393 gbgss37.seq
209715971 gbgss38.seq
209718123 gbgss39.seq
209716210 gbgss4.seq
209717394 gbgss40.seq
209716993 gbgss41.seq
209717573 gbgss42.seq
209717820 gbgss43.seq
209719592 gbgss44.seq
209717695 gbgss45.seq
209716211 gbgss46.seq
209717274 gbgss47.seq
209716732 gbgss48.seq
209716710 gbgss49.seq
209718523 gbgss5.seq
76194077 gbgss50.seq
250001685 gbgss51.seq
250002829 gbgss52.seq
250001767 gbgss53.seq
250000482 gbgss54.seq
250000342 gbgss55.seq
250003223 gbgss56.seq
250004758 gbgss57.seq
250001030 gbgss58.seq
88051417 gbgss59.seq
209716450 gbgss6.seq
209716515 gbgss7.seq
209718215 gbgss8.seq
209716168 gbgss9.seq
250000286 gbhtc1.seq
1336449 gbhtc2.seq
250187848 gbhtg1.seq
250221274 gbhtg10.seq
250167405 gbhtg11.seq
250120645 gbhtg12.seq
250289012 gbhtg13.seq
250127914 gbhtg14.seq
250005405 gbhtg15.seq
250094232 gbhtg16.seq
250115051 gbhtg17.seq
250055858 gbhtg18.seq
250095005 gbhtg19.seq
250149911 gbhtg2.seq
250208235 gbhtg20.seq
250215319 gbhtg21.seq
250146697 gbhtg22.seq
250817091 gbhtg23.seq
250216293 gbhtg24.seq
250125005 gbhtg25.seq
250129335 gbhtg26.seq
250318354 gbhtg27.seq
250249935 gbhtg28.seq
250107952 gbhtg29.seq
250186549 gbhtg3.seq
250067973 gbhtg30.seq
250148637 gbhtg31.seq
250158670 gbhtg32.seq
250083587 gbhtg33.seq
250417854 gbhtg34.seq
250136103 gbhtg35.seq
250049014 gbhtg36.seq
250019132 gbhtg37.seq
250099633 gbhtg38.seq
250198320 gbhtg39.seq
250220555 gbhtg4.seq
250098681 gbhtg40.seq
250168028 gbhtg41.seq
250265502 gbhtg42.seq
250056902 gbhtg43.seq
250006041 gbhtg44.seq
250125834 gbhtg45.seq
250037642 gbhtg46.seq
250198044 gbhtg47.seq
250136668 gbhtg48.seq
250105554 gbhtg49.seq
250123070 gbhtg5.seq
250004951 gbhtg50.seq
250080686 gbhtg51.seq
250011200 gbhtg52.seq
250163982 gbhtg53.seq
250029185 gbhtg54.seq
250137551 gbhtg55.seq
103133623 gbhtg56.seq
250116110 gbhtg6.seq
250007637 gbhtg7.seq
250035917 gbhtg8.seq
250013167 gbhtg9.seq
250181532 gbinv1.seq
250308874 gbinv2.seq
250002399 gbinv3.seq
250000396 gbinv4.seq
130139020 gbinv5.seq
496094459 gbjou.idx
444631903 gbkey.idx
144228891 gbmam.seq
24705216 gbnew.txt
250000658 gbpat1.seq
250001358 gbpat2.seq
250019093 gbpat3.seq
250000692 gbpat4.seq
250000305 gbpat5.seq
168890409 gbpat6.seq
19121376 gbphg.seq
250085350 gbpln1.seq
250002299 gbpln2.seq
250015426 gbpln3.seq
250002318 gbpln4.seq
250003288 gbpln5.seq
123570558 gbpln6.seq
250032724 gbpri1.seq
250227843 gbpri10.seq
250190135 gbpri11.seq
250000149 gbpri12.seq
250100369 gbpri13.seq
250113818 gbpri14.seq
250016780 gbpri15.seq
250144444 gbpri16.seq
250147096 gbpri17.seq
250054768 gbpri18.seq
250102401 gbpri19.seq
250170026 gbpri2.seq
250115008 gbpri20.seq
250000694 gbpri21.seq
250000467 gbpri22.seq
176486476 gbpri23.seq
250205029 gbpri3.seq
250092405 gbpri4.seq
250160680 gbpri5.seq
250121208 gbpri6.seq
250119483 gbpri7.seq
250085919 gbpri8.seq
250099549 gbpri9.seq
138325 gbrel.txt
250205841 gbrod1.seq
250037619 gbrod2.seq
250128855 gbrod3.seq
250001219 gbrod4.seq
154192731 gbrod5.seq
1584672544 gbsdr.txt
1441118 gbsec.idx
250001159 gbsts1.seq
168397121 gbsts2.seq
119267258 gbsup.seq
32875125 gbsyn.seq
1415474 gbuna.seq
250002281 gbvrl1.seq
250220557 gbvrl2.seq
68209298 gbvrl3.seq
250081919 gbvrt1.seq
65976039 gbvrt2.seq
2.2.6 Per-Division Statistics
The following table provides a per-division breakdown of the number of
sequence entries and the total number of bases of DNA/RNA in each sequence
data file:
Division Entries Bases
BCT1 20383 103232685
BCT2 17561 103377992
BCT3 54095 90206136
BCT4 25754 104748091
BCT5 35212 93782212
BCT6 9861 11591632
EST1 68496 26433639
EST10 76707 29913278
EST100 69837 28641168
EST101 70965 32276912
EST102 64306 34128421
EST103 67600 39770265
EST104 72399 48009460
EST105 76139 29903506
EST106 75274 32900058
EST107 75584 27528715
EST108 74059 35364166
EST109 68231 37517508
EST11 75682 28784338
EST110 76829 42212448
EST111 80117 45010500
EST112 73344 48596024
EST113 68392 40704976
EST114 72196 48929349
EST115 70971 44620255
EST116 72083 45759339
EST117 74830 41315321
EST118 74973 48415330
EST119 74740 49636229
EST12 77323 30838122
EST120 70943 47423014
EST121 80642 43249793
EST122 75247 24366808
EST123 81720 45170477
EST124 76966 43913098
EST125 72887 43879501
EST126 64884 31368006
EST127 72071 39963723
EST128 66888 36386979
EST129 69797 42708364
EST13 77175 29195165
EST130 72791 41947303
EST131 68894 43006940
EST132 69177 41590302
EST133 74829 43385132
EST134 68610 41393161
EST135 59562 34049755
EST136 99216 53656327
EST137 84201 48735245
EST138 71708 36712957
EST139 72655 38828291
EST14 79470 32355163
EST140 106889 56840696
EST141 100044 55777176
EST142 75108 45301585
EST143 68811 34246925
EST144 64068 29419080
EST145 55623 28655792
EST146 65884 32443652
EST147 60670 30664386
EST148 69066 37262934
EST149 70375 50115100
EST15 73279 30952207
EST150 67700 47162562
EST151 79797 46398164
EST152 58406 30135433
EST153 63774 32563599
EST154 67656 39349783
EST155 66410 44032922
EST156 63015 37331335
EST157 75753 40769296
EST158 63986 44082465
EST159 70574 38881062
EST16 75515 33319155
EST160 59603 41629201
EST161 69972 33857718
EST162 74021 26118196
EST163 72783 46917614
EST164 73768 38059249
EST165 61472 31729616
EST166 71542 50838212
EST167 68408 46347966
EST168 68542 35178304
EST169 69313 46345967
EST17 83449 34138337
EST170 69392 52302976
EST171 69143 36267196
EST172 72395 48864734
EST173 71530 56339368
EST174 62376 41197637
EST175 64110 36695183
EST176 60089 34072781
EST177 75477 41113683
EST178 84001 54658628
EST179 72684 42990594
EST18 80240 32372093
EST180 105559 66154422
EST181 107867 41723265
EST182 88759 41424569
EST183 87596 28655379
EST184 70622 25024678
EST185 74303 27882253
EST186 74426 26273089
EST187 79826 27206048
EST188 73743 27153316
EST189 68814 29407870
EST19 79310 32743500
EST190 33537 11275665
EST2 75261 28892385
EST20 74064 29744963
EST21 73785 34286453
EST22 75880 30328478
EST23 77327 32341211
EST24 75764 34023665
EST25 71973 30570097
EST26 76064 31586135
EST27 76827 33252062
EST28 102807 48919068
EST29 71009 47776534
EST3 74009 30036373
EST30 82825 55706239
EST31 90694 50528881
EST32 96193 50082429
EST33 97323 44225862
EST34 95351 49410481
EST35 93790 40277186
EST36 59406 16100121
EST37 59645 15912658
EST38 70884 20486615
EST39 45726 13073187
EST4 74418 28188493
EST40 43479 11781607
EST41 43096 12100092
EST42 43129 11254236
EST43 94330 41261744
EST44 94757 43612310
EST45 92249 48171215
EST46 88127 41876030
EST47 106844 56355998
EST48 85639 40662755
EST49 73098 30732456
EST5 48589 15395243
EST50 72653 32319855
EST51 71236 30980987
EST52 73574 30973262
EST53 81896 32245461
EST54 69189 27018692
EST55 65511 30220622
EST56 74254 31902722
EST57 77914 35471982
EST58 74910 32662028
EST59 74387 26736760
EST6 56169 18128738
EST60 83645 35020610
EST61 61013 24263956
EST62 40155 11138780
EST63 40163 11941628
EST64 40438 12632193
EST65 40641 12104220
EST66 40512 12872722
EST67 40586 12708509
EST68 40502 12253099
EST69 40206 12301720
EST7 74539 29341496
EST70 40519 12465381
EST71 41420 12006933
EST72 41185 12832838
EST73 41138 12863939
EST74 41074 13254597
EST75 44798 12086045
EST76 41733 22902142
EST77 41381 23170484
EST78 42536 17467220
EST79 45771 21049114
EST8 76370 30726997
EST80 50553 20895962
EST81 47854 20639217
EST82 74671 32430918
EST83 74122 29005235
EST84 72962 30403517
EST85 77491 44462577
EST86 78367 41568292
EST87 76243 40764209
EST88 78960 37695220
EST89 70099 40713271
EST9 77709 29988701
EST90 74476 36160099
EST91 75416 38467675
EST92 70594 37016361
EST93 77620 49741074
EST94 68120 36031266
EST95 71944 36302067
EST96 72950 38530579
EST97 73801 43942432
EST98 68052 45428838
EST99 75480 43830838
GSS1 83510 35769523
GSS10 67402 34654546
GSS11 69545 40716742
GSS12 61852 31727775
GSS13 66515 35000942
GSS14 69160 35545413
GSS15 65641 29622920
GSS16 63401 29884671
GSS17 73134 43761198
GSS18 65435 32197792
GSS19 59314 26993250
GSS2 83801 35919022
GSS20 52055 27424135
GSS21 52705 25722081
GSS22 53781 22942685
GSS23 58137 35735522
GSS24 58466 28312906
GSS25 53013 24887174
GSS26 61950 40285643
GSS27 63160 26209543
GSS28 53791 22864357
GSS29 56968 28036000
GSS3 82137 38487974
GSS30 65133 31276459
GSS31 58059 33522731
GSS32 84168 36972101
GSS33 69768 37108177
GSS34 67438 40104511
GSS35 65648 40921372
GSS36 74586 36234060
GSS37 70033 37023509
GSS38 73018 39254391
GSS39 86274 57314607
GSS4 74475 38231630
GSS40 86276 57312096
GSS41 81024 42198242
GSS42 83061 47903062
GSS43 80048 36910081
GSS44 75835 25892318
GSS45 74245 52153021
GSS46 73935 52654571
GSS47 68305 46906194
GSS48 66272 43852670
GSS49 66340 43719081
GSS5 71303 38144636
GSS50 25699 13393491
GSS51 88406 66834201
GSS52 84709 63676672
GSS53 76088 41277744
GSS54 82476 64094710
GSS55 70546 59050369
GSS56 69679 63115984
GSS57 60648 57103972
GSS58 108163 54474634
GSS59 33889 15094020
GSS6 70672 35444207
GSS7 71437 35836305
GSS8 71450 36555732
GSS9 69017 34317658
HTC1 39733 50920907
HTC2 274 514038
HTG1 1324 190978205
HTG10 1084 191253778
HTG11 1458 187277951
HTG12 1229 190066705
HTG13 758 192816439
HTG14 661 192854250
HTG15 700 192708435
HTG16 692 192899493
HTG17 775 192601076
HTG18 672 192739270
HTG19 785 192629366
HTG2 1743 188517557
HTG20 2173 177493171
HTG21 1101 188538506
HTG22 1162 188966621
HTG23 972 191135401
HTG24 745 192582759
HTG25 933 190834655
HTG26 979 190498167
HTG27 936 191062031
HTG28 828 191731339
HTG29 740 192599360
HTG3 2659 187705373
HTG30 993 190368601
HTG31 816 192019886
HTG32 961 190873631
HTG33 1162 188320898
HTG34 1065 189799612
HTG35 1067 189654612
HTG36 1113 189016067
HTG37 1032 190110850
HTG38 951 192364341
HTG39 1135 189477923
HTG4 3181 190023183
HTG40 1051 191559049
HTG41 889 191909332
HTG42 841 192925288
HTG43 877 191868067
HTG44 824 192305579
HTG45 925 191281511
HTG46 1074 190238615
HTG47 968 191888710
HTG48 1099 190039997
HTG49 1581 186078393
HTG5 1270 188752257
HTG50 1544 187536381
HTG51 1126 192902340
HTG52 961 194595989
HTG53 1048 193402667
HTG54 1230 190490333
HTG55 1413 194474575
HTG56 441 73942626
HTG6 1288 187930907
HTG7 1239 188431111
HTG8 1240 188193135
HTG9 1306 187848061
INV1 8528 176138105
INV2 1850 165049452
INV3 65819 85885430
INV4 39467 115336766
INV5 20628 56375617
MAM 42995 49199549
PAT1 222798 70208547
PAT2 156725 88003918
PAT3 120112 108897629
PAT4 138316 91316635
PAT5 121374 50071275
PAT6 115720 41567433
PHG 2220 7284466
PLN1 17611 143259268
PLN2 76084 82576945
PLN3 32426 133847803
PLN4 42926 94972670
PLN5 51474 105951356
PLN6 20122 51628724
PRI1 13398 156076517
PRI10 1304 174976075
PRI11 1390 174845906
PRI12 1646 177871996
PRI13 32151 136317404
PRI14 34007 123303751
PRI15 1609 178715779
PRI16 1672 180830631
PRI17 1984 183395340
PRI18 1874 186788954
PRI19 26412 135662049
PRI2 1422 173845151
PRI20 13514 166625208
PRI21 43039 123729345
PRI22 31719 131063632
PRI23 42387 69152716
PRI3 1263 183090770
PRI4 1250 176183870
PRI5 1149 175264825
PRI6 1231 180884435
PRI7 1205 172736616
PRI8 1286 170138041
PRI9 1337 177255462
ROD1 6321 181283393
ROD2 22528 157524303
ROD3 1209 194697603
ROD4 20557 152687659
ROD5 40839 53671170
STS1 89988 35787549
STS2 64851 29899794
SUP 19345 32176331
SYN 7220 13493248
UNA 612 329899
VRL1 74376 63454470
VRL2 77773 62734011
VRL3 15920 23399860
VRT1 65841 92114769
VRT2 20239 20088586
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 132.0 (chloroplast and mitochon-
drial sequences not included):
Entries Bases Species
6254226 9261832326 Homo sapiens
642958 5255217048 Rattus norvegicus
3835703 4684588193 Mus musculus
340327 687489528 Drosophila melanogaster
163827 505321990 Oryza sativa (japonica cultivar-group)
411404 361863676 Arabidopsis thaliana
469403 316282621 Brassica oleracea
309735 308436293 Danio rerio
196537 220486873 Caenorhabditis elegans
300732 175611544 Ciona intestinalis
189145 170122236 Tetraodon nigroviridis
160895 167110961 Pan troglodytes
340240 157123549 Zea mays
275511 152279736 Hordeum vulgare
304584 141823745 Glycine max
245572 133601754 Bos taurus
259391 132563617 Triticum aestivum
235985 131090717 Xenopus laevis
174874 121919564 Medicago truncatula
155382 96004474 Anopheles gambiae
2.2.8 Growth of GenBank
The following table lists the number of bases and the number of sequence
records in each release of GenBank, beginning with Release 3 in 1982.
From 1982 to the present, the number of bases in GenBank has doubled
approximately every 14 months.
Release Date Base Pairs Entries
3 Dec 1982 680338 606
14 Nov 1983 2274029 2427
20 May 1984 3002088 3665
24 Sep 1984 3323270 4135
25 Oct 1984 3368765 4175
26 Nov 1984 3689752 4393
32 May 1985 4211931 4954
36 Sep 1985 5204420 5700
40 Feb 1986 5925429 6642
42 May 1986 6765476 7416
44 Aug 1986 8442357 8823
46 Nov 1986 9615371 9978
48 Feb 1987 10961380 10913
50 May 1987 13048473 12534
52 Aug 1987 14855145 14020
53 Sep 1987 15514776 14584
54 Dec 1987 16752872 15465
55 Mar 1988 19156002 17047
56 Jun 1988 20795279 18226
57 Sep 1988 22019698 19044
57.1 Oct 1988 23800000 20579
58 Dec 1988 24690876 21248
59 Mar 1989 26382491 22479
60 Jun 1989 31808784 26317
61 Sep 1989 34762585 28791
62 Dec 1989 37183950 31229
63 Mar 1990 40127752 33377
64 Jun 1990 42495893 35100
65 Sep 1990 49179285 39533
66 Dec 1990 51306092 41057
67 Mar 1991 55169276 43903
68 Jun 1991 65868799 51418
69 Sep 1991 71947426 55627
70 Dec 1991 77337678 58952
71 Mar 1992 83894652 65100
72 Jun 1992 92160761 71280
73 Sep 1992 101008486 78608
74 Dec 1992 120242234 97084
75 Feb 1993 126212259 106684
76 Apr 1993 129968355 111911
77 Jun 1993 138904393 120134
78 Aug 1993 147215633 131328
79 Oct 1993 157152442 143492
80 Dec 1993 163802597 150744
81 Feb 1994 173261500 162946
82 Apr 1994 180589455 169896
83 Jun 1994 191393939 182753
84 Aug 1994 201815802 196703
85 Oct 1994 217102462 215273
86 Dec 1994 230485928 237775
87 Feb 1995 248499214 269478
88 Apr 1995 286094556 352414
89 Jun 1995 318624568 425211
90 Aug 1995 353713490 492483
91 Oct 1995 384939485 555694
92 Dec 1995 425860958 620765
93 Feb 1996 463758833 685693
94 Apr 1996 499127741 744295
95 Jun 1996 551750920 835487
96 Aug 1996 602072354 920588
97 Oct 1996 651972984 1021211
98 Dec 1996 730552938 1114581
99 Feb 1997 786898138 1192505
100 Apr 1997 842864309 1274747
101 Jun 1997 966993087 1491069
102 Aug 1997 1053474516 1610848
103 Oct 1997 1160300687 1765847
104 Dec 1997 1258290513 1891953
105 Feb 1998 1372368913 2042325
106 Apr 1998 1502542306 2209232
107 Jun 1998 1622041465 2355928
108 Aug 1998 1797137713 2532359
109 Oct 1998 2008761784 2837897
110 Dec 1998 2162067871 3043729
111 Apr 1999 2569578208 3525418
112 Jun 1999 2974791993 4028171
113 Aug 1999 3400237391 4610118
114 Oct 1999 3841163011 4864570
115 Dec 1999 4653932745 5354511
116 Feb 2000 5805414935 5691170
117 Apr 2000 7376080723 6215002
118 Jun 2000 8604221980 7077491
119 Aug 2000 9545724824 8214339
120 Oct 2000 10335692655 9102634
121 Dec 2000 11101066288 10106023
122 Feb 2001 11720120326 10896781
123 Apr 2001 12418544023 11545572
124 Jun 2001 12973707065 12243766
125 Aug 2001 13543364296 12813516
126 Oct 2001 14396883064 13602262
127 Dec 2001 15849921438 14976310
128 Feb 2002 17089143893 15465325
129 Apr 2002 19072679701 16769983
130 Jun 2002 20648748345 17471130
131 Aug 2002 22616937182 18197119
132 Oct 2002 26525934656 19808101
3. FILE FORMATS
The flat file examples included in this section, while not always from the
current release, are usually fairly recent. Any differences compared to the
actual records are the result of updates to the entries involved.
3.1 File Header Information
With the exception of the index files, each of the 390 files of a
GenBank release begins with the same header, except for the first line,
which contains the file name, and the sixth line, which contains the
title of the file. The first line of the file contains the file name
in character positions 1 to 9 and the full database name (Genetic Sequence
Data Bank) starting in column 22. The brief names of the files in this
release are listed in section 2.2.
The second line contains the date of the current release in the form
`day month year', beginning in position 27. The fourth line contains
the current GenBank release number. The release number appears in
positions 48 to 52 and consists of three numbers separated by a decimal
point. The number to the left of the decimal is the major release
number. The digit to the right of the decimal indicates the version of
the major release; it is zero for the first version. The sixth line
contains a title for the file. The eighth line lists the number of
entries (loci), number of bases (or base pairs), and number of reports
of sequences (equal to number of entries in this case). These numbers are
right-justified at fixed positions. The number of entries appears in
positions 1 to 8, the number of bases in positions 16 to 26, and the
number of reports in positions 40 to 47. The third, fifth, seventh, and
ninth lines are blank.
1 10 20 30 40 50 60 70 79
---------+---------+---------+---------+---------+---------+---------+---------
GBBCT1.SEQ Genetic Sequence Data Bank
15 April 2002
NCBI-GenBank Flat File Release 132.0
Bacterial Sequences (Part 1)
37811 loci, 97585608 bases, from 37811 reported sequences
---------+---------+---------+---------+---------+---------+---------+---------
1 10 20 30 40 50 60 70 79
Example 1. Sample File Header
3.2 Directory Files
3.2.1 Short Directory File
The short directory file contains brief descriptions of all of the
sequence entries contained in this release. These descriptions are in
fifteen groups, one group for each of the fifteen sequence entry
data files. The first record at the beginning of a group of entries
contains the name of the group in uppercase characters, beginning in
position 21. The organism groups are PRIMATE, RODENT, OTHER MAMMAL,
OTHER VERTEBRATE, INVERTEBRATE, PLANT, BACTERIAL, STRUCTURAL RNA, VIRAL,
PHAGE, SYNTHETIC, UNANNOTATED, EXPRESSED SEQUENCE TAG, PATENT, or
SEQUENCE TAGGED SITE. The second record is blank.
Each record in the short directory contains the sequence entry name
(LOCUS) in the first 12 positions, followed by a brief definition of
the sequence beginning in column 13. The definition is truncated (at
the end of a word) to leave room at the right margin for at least one
space, the sequence length, and the letters `bp'. The length of the
sequence is printed right-justified to column 77, followed by the
letters `bp' in columns 78 and 79. The next-to-last record for a group
has `ZZZZZZZZZZ' in its first ten positions (where the entry name
would normally appear). The last record is a blank line. An example of
the short directory file format, showing the descriptions of the last
entries in the Other Vertebrate sequence data file and the first
entries of the Invertebrate sequence data file, is reproduced below:
1 10 20 30 40 50 60 70 79
---------+---------+---------+---------+---------+---------+---------+---------
ZEFWNT1G3 B.rerio wnt-1 gene (exon 3) for wnt-1 protein. 266bp
ZEFWNT1G4 B.rerio wnt-1 gene (exon 4) for wnt-1 protein. 647bp
ZEFZF54 Zebrafish homeotic gene ZF-54. 246bp
ZEFZFEN Zebrafish engrailed-like homeobox sequence. 327bp
ZZZZZZZZZZ
INVERTEBRATE
AAHAV33A Acanthocheilonema viteae pepsin-inhibitor-like-protein 1048bp
ACAAC01 Acanthamoeba castelani gene encoding actin I. 1571bp
ACAACTPH Acanthamoeba castellanii actophorin mRNA, complete cds. 671bp
ACAMHCA A.castellanii non-muscle myosin heavy chain gene, partial 5894bp
---------+---------+---------+---------+---------+---------+---------+---------
1 10 20 30 40 50 60 70 79
Example 2. Short Directory File
3.3 Index Files
There are six files containing indices to the entries in this release:
Accession number index file (Accession and Version)
Secondary accession number index file
Keyword phrase index file
Author name index file
Journal citation index file
Gene name index file
The index keys (accession numbers, keywords, authors, journals, and
gene symbols.) of an index are sorted alphabetically. All index keys
appear in uppercase characters even though they appear in mixed case
in the sequence entries. Following each index key, the identifiers of the
sequence entries containing that key are listed (LOCUS name,
division abbreviation, and primary accession number). The division
abbreviations are:
1. PRI - primate sequences
2. ROD - rodent sequences
3. MAM - other mammalian sequences
4. VRT - other vertebrate sequences
5. INV - invertebrate sequences
6. PLN - plant, fungal, and algal sequences
7. BCT - bacterial sequences
8. VRL - viral sequences
9. PHG - bacteriophage sequences
10. SYN - synthetic sequences
11. UNA - unannotated sequences
12. EST - EST sequences (expressed sequence tags)
13. PAT - patent sequences
14. STS - STS sequences (sequence tagged sites)
15. GSS - GSS sequences (genome survey sequences)
16. HTG - HTGS sequences (high throughput genomic sequences)
17. HTC - HTC sequences (high throughput cDNA sequences)
A line-oriented, TAB-delimited format is utilized for the gbaut.idx,
gbgen.idx, gbjou.idx, gbkey.idx, and gbsec.idx indexes. Each index
key is presented on its own line, and is followed by a
LOCUS/Division/Accession triplet for every record containing the key:
Indexed-Term
LOCUS-name1 Div-code1 Accession1
LOCUS-name2 Div-code2 Accession2
LOCUS-name3 Div-code3 Accession3
....
Here is an example of the format, in which TAB characters are displayed
as ^I, and carriage-returns/newlines as $ :
(H+,K+)-ATPASE BETA-SUBUNIT$
^IRATHKATPB^IROD^IM55655$
^IMUSATP4B1^IROD^IM64685$
^IMUSATP4B2^IROD^IM64686$
^IMUSATP4B3^IROD^IM64687$
^IMUSATP4B4^IROD^IM64688$
^IDOGATPASEB^IMAM^IM76486$
When viewed by a file browser such as 'less' or 'more' :
(H+,K+)-ATPASE BETA-SUBUNIT
RATHKATPB ROD M55655
MUSATP4B1 ROD M64685
MUSATP4B2 ROD M64686
MUSATP4B3 ROD M64687
MUSATP4B4 ROD M64688
DOGATPASEB MAM M76486
Note that the index keys can be distinguished from LOCUS/DIV/ACCESSION
by the fact that they do not start with a TAB character. So one can
extract just the terms via simple text-processing:
perl -ne 'print unless /^\s+/' < gbkey.idx > terms.gbkey
The format of the primary accession number index file is slightly
different, with each indexed key (Accession.Version) present on
the same line as the LOCUS/Division/Accession triplet:
Accession1.Version1 Locus-name1 Div-code1 Accession1
Accession2.Version2 Locus-name2 Div-code2 Accession2
....
Here is an example of the format, in which TAB characters are displayed
as ^I, and carriage-returns/newlines as $ :
AC000102.1^IAC000102^IPRI^IAC000102$
AC000103.1^IAC000103^IPLN^IAC000103$
AC000104.1^IF19P19^IPLN^IAC000104$
AC000105.40^IAC000105^IPRI^IAC000105$
AC000106.1^IF7G19^IPLN^IAC000106$
AC000107.1^IAC000107^IPLN^IAC000107$
AC000108.1^IAC000108^IBCT^IAC000108$
AC000109.1^IHSAC000109^IPRI^IAC000109$
AC000110.1^IHSAC000110^IPRI^IAC000110$
When viewed by a file browser such as 'less' or 'more' :
AC000102.1 AC000102 PRI AC000102
AC000103.1 AC000103 PLN AC000103
AC000104.1 F19P19 PLN AC000104
AC000105.40 AC000105 PRI AC000105
AC000106.1 F7G19 PLN AC000106
AC000107.1 AC000107 PLN AC000107
AC000108.1 AC000108 BCT AC000108
AC000109.1 HSAC000109 PRI AC000109
AC000110.1 HSAC000110 PRI AC000110
3.3.1 Accession Number Index File - gbacc.idx
Accession numbers are unique six character or eight-character alphanumeric
identifiers of GenBank database entries. The six-character accession
number format consists of a single uppercase letter, followed by 5 digits.
The eight-character accession number format consists of two uppercase
letters, followed by 6 digits. Accessions provide an unchanging identifier
for the data with which they are associated, and we encourage you to cite
accession numbers whenever you refer to data from GenBank.
GenBank entries can have both 'primary' and 'secondary' accessions
associated with them (see Section 3.5.6). Only primary accessions are present
in the gbacc.idx index.
3.3.2 Keyword Phrase Index File - gbkey.idx
Keyword phrases consist of names for gene products and other
characteristics of sequence entries.
3.3.3 Author Name Index File - gbaut*.idx
The author name index files list all of the author names that appear
in the references within sequence records.
3.3.4 Journal Citation Index File - gbjou.idx
The journal citation index file lists all of the citations that appear
in the references within sequence records.. All citations are truncated
to 80 characters.
3.3.5 Gene Name Index - gbgen.idx
The /gene qualifiers of many GenBank entries contain values other than
official gene symbols, such as the product or the standard name of the gene.
Hence, NCBI has chosen to build an index (gbgen.idx) more like a keyword index
for this field, using both the GenBank /gene qualifier and the 'Gene.locus'
fields from the NCBI internal database as keys.
3.4 Sequence Entry Files
GenBank releases contain one or more sequence entry data files, one
for each "division" of GenBank.
3.4.1 File Organization
Each of these files has the same format and consists of two parts:
header information (described in section 3.1) and sequence entries for
that division (described in the following sections).
3.4.2 Entry Organization
In the second portion of a sequence entry file (containing the
sequence entries for that division), each record (line) consists of
two parts. The first part is found in positions 1 to 10 and may
contain:
1. A keyword, beginning in column 1 of the record (e.g., REFERENCE is
a keyword).
2. A subkeyword beginning in column 3, with columns 1 and 2 blank
(e.g., AUTHORS is a subkeyword of REFERENCE). Or a subkeyword beginning
in column 4, with columns 1, 2, and 3 blank (e.g., PUBMED is a
subkeyword of REFERENCE).
3. Blank characters, indicating that this record is a continuation of
the information under the keyword or subkeyword above it.
4. A code, beginning in column 6, indicating the nature of an entry
(feature key) in the FEATURES table; these codes are described in
Section 3.4.12.1 below.
5. A number, ending in column 9 of the record. This number occurs in
the portion of the entry describing the actual nucleotide sequence and
designates the numbering of sequence positions.
6. Two slashes (//) in positions 1 and 2, marking the end of an entry.
The second part of each sequence entry record contains the information
appropriate to its keyword, in positions 13 to 80 for keywords and
positions 11 to 80 for the sequence.
The following is a brief description of each entry field. Detailed
information about each field may be found in Sections 3.4.4 to 3.4.14.
LOCUS - A short mnemonic name for the entry, chosen to suggest the
sequence's definition. Mandatory keyword/exactly one record.
DEFINITION - A concise description of the sequence. Mandatory
keyword/one or more records.
ACCESSION - The primary accession number is a unique, unchanging
code assigned to each entry. (Please use this code when citing
information from GenBank.) Mandatory keyword/one or more records.
VERSION - A compound identifier consisting of the primary
accession number and a numeric version number associated with the
current version of the sequence data in the record. This is followed
by an integer key (a "GI") assigned to the sequence by NCBI.
Mandatory keyword/exactly one record.
NID - An alternative method of presenting the NCBI GI
identifier (described above). The NID is obsolete and was removed
from the GenBank flatfile format in December 1999.
KEYWORDS - Short phrases describing gene products and other
information about an entry. Mandatory keyword in all annotated
entries/one or more records.
SEGMENT - Information on the order in which this entry appears in a
series of discontinuous sequences from the same molecule. Optional
keyword (only in segmented entries)/exactly one record.
SOURCE - Common name of the organism or the name most frequently used
in the literature. Mandatory keyword in all annotated entries/one or
more records/includes one subkeyword.
ORGANISM - Formal scientific name of the organism (first line)
and taxonomic classification levels (second and subsequent lines).
Mandatory subkeyword in all annotated entries/two or more records.
REFERENCE - Citations for all articles containing data reported
in this entry. Includes seven subkeywords and may repeat. Mandatory
keyword/one or more records.
AUTHORS - Lists the authors of the citation. Optional
subkeyword/one or more records.
CONSRTM - Lists the collective names of consortiums associated
with the citation (eg, International Human Genome Sequencing Consortium),
rather than individual author names. Optional subkeyword/one or more records.
TITLE - Full title of citation. Optional subkeyword (present
in all but unpublished citations)/one or more records.
JOURNAL - Lists the journal name, volume, year, and page
numbers of the citation. Mandatory subkeyword/one or more records.
MEDLINE - Provides the Medline unique identifier for a
citation. Optional subkeyword/one record.
PUBMED - Provides the PubMed unique identifier for a
citation. Optional subkeyword/one record.
REMARK - Specifies the relevance of a citation to an
entry. Optional subkeyword/one or more records.
COMMENT - Cross-references to other sequence entries, comparisons to
other collections, notes of changes in LOCUS names, and other remarks.
Optional keyword/one or more records/may include blank records.
FEATURES - Table containing information on portions of the
sequence that code for proteins and RNA molecules and information on
experimentally determined sites of biological significance. Optional
keyword/one or more records.
BASE COUNT - Summary of the number of occurrences of each base
code in the sequence. Mandatory keyword/exactly one record.
ORIGIN - Specification of how the first base of the reported sequence
is operationally located within the genome. Where possible, this
includes its location within a larger genetic map. Mandatory
keyword/exactly one record.
- The ORIGIN line is followed by sequence data (multiple records).
// - Entry termination symbol. Mandatory at the end of an
entry/exactly one record.
3.4.3 Sample Sequence Data File
An example of a complete sequence entry file follows. (This example
has only two entries.) Note that in this example, as throughout the
data bank, numbers in square brackets indicate items in the REFERENCE
list. For example, in ACARR58S, [1] refers to the paper by Mackay, et
al.
1 10 20 30 40 50 60 70 79
---------+---------+---------+---------+---------+---------+---------+---------
GBSMP.SEQ Genetic Sequence Data Bank
15 December 1992
GenBank Flat File Release 74.0
Structural RNA Sequences
2 loci, 236 bases, from 2 reported sequences
LOCUS AAURRA 118 bp ss-rRNA RNA 16-JUN-1986
DEFINITION A.auricula-judae (mushroom) 5S ribosomal RNA.
ACCESSION K03160
VERSION K03160.1 GI:173593
KEYWORDS 5S ribosomal RNA; ribosomal RNA.
SOURCE A.auricula-judae (mushroom) ribosomal RNA.
ORGANISM Auricularia auricula-judae
Eukaryota; Fungi; Eumycota; Basidiomycotina; Phragmobasidiomycetes;
Heterobasidiomycetidae; Auriculariales; Auriculariaceae.
REFERENCE 1 (bases 1 to 118)
AUTHORS Huysmans,E., Dams,E., Vandenberghe,A. and De Wachter,R.
TITLE The nucleotide sequences of the 5S rRNAs of four mushrooms and
their use in studying the phylogenetic position of basidiomycetes
among the eukaryotes
JOURNAL Nucleic Acids Res. 11, 2871-2880 (1983)
FEATURES Location/Qualifiers
rRNA 1..118
/note="5S ribosomal RNA"
BASE COUNT 27 a 34 c 34 g 23 t
ORIGIN 5' end of mature rRNA.
1 atccacggcc ataggactct gaaagcactg catcccgtcc gatctgcaaa gttaaccaga
61 gtaccgccca gttagtacca cggtggggga ccacgcggga atcctgggtg ctgtggtt
//
LOCUS ABCRRAA 118 bp ss-rRNA RNA 15-SEP-1990
DEFINITION Acetobacter sp. (strain MB 58) 5S ribosomal RNA, complete sequence.
ACCESSION M34766
VERSION M34766.1 GI:173603
KEYWORDS 5S ribosomal RNA.
SOURCE Acetobacter sp. (strain MB 58) rRNA.
ORGANISM Acetobacter sp.
Prokaryotae; Gracilicutes; Scotobacteria; Aerobic rods and cocci;
Azotobacteraceae.
REFERENCE 1 (bases 1 to 118)
AUTHORS Bulygina,E.S., Galchenko,V.F., Govorukhina,N.I., Netrusov,A.I.,
Nikitin,D.I., Trotsenko,Y.A. and Chumakov,K.M.
TITLE Taxonomic studies of methylotrophic bacteria by 5S ribosomal RNA
sequencing
JOURNAL J. Gen. Microbiol. 136, 441-446 (1990)
FEATURES Location/Qualifiers
rRNA 1..118
/note="5S ribosomal RNA"
BASE COUNT 27 a 40 c 32 g 17 t 2 others
ORIGIN
1 gatctggtgg ccatggcggg agcaaatcag ccgatcccat cccgaactcg gccgtcaaat
61 gccccagcgc ccatgatact ctgcctcaag gcacggaaaa gtcggtcgcc gccagayy
//
---------+---------+---------+---------+---------+---------+---------+---------
1 10 20 30 40 50 60 70 79
Example 9. Sample Sequence Data File
3.4.4 LOCUS Format
The items of information contained in the LOCUS record are always
found in fixed positions. The locus name (or entry name), which is
always sixteen characters or less, begins in position 13. The locus name
is designed to help group entries with similar sequences: the first
three characters usually designate the organism; the fourth and fifth
characters can be used to show other group designations, such as gene
product; for segmented entries the last character is one of a series
of sequential integers.
The number of bases or base pairs in the sequence ends in position 40.
The letters `bp' are in positions 42 to 43. Positions 45 to 47 provide
the number of strands of the sequence. Positions 48 to 53 indicate the
type of molecule sequenced. Topology of the molecule is indicated in
positions 56 to 63.
GenBank sequence entries are divided among many different
'divisions'. Each entry's division is specified by a three-letter code
in positions 65 to 67. See Section 3.3 for an explanation of division
codes.
Positions 69 to 79 of the record contain the date the entry was
entered or underwent any substantial revisions, such as the addition
of newly published data, in the form dd-MMM-yyyy.
The detailed format for the LOCUS line format is as follows:
Positions Contents
--------- --------
01-05 'LOCUS'
06-12 spaces
13-28 Locus name
29-29 space
30-40 Length of sequence, right-justified
41-41 space
42-43 bp
44-44 space
45-47 spaces, ss- (single-stranded), ds- (double-stranded), or
ms- (mixed-stranded)
48-53 NA, DNA, RNA, tRNA (transfer RNA), rRNA (ribosomal RNA),
mRNA (messenger RNA), uRNA (small nuclear RNA), snRNA,
snoRNA. Left justified.
54-55 space
56-63 'linear' followed by two spaces, or 'circular'
64-64 space
65-67 The division code (see Section 3.3)
68-68 space
69-79 Date, in the form dd-MMM-yyyy (e.g., 15-MAR-1991)
Although each of these data values can be found at column-specific
positions, we encourage those who parse the contents of the LOCUS
line to use a token-based approach. This will prevent the need for
software changes if the spacing of the data values ever has to be
modified.
3.4.5 DEFINITION Format
The DEFINITION record gives a brief description of the sequence,
proceeding from general to specific. It starts with the common name of
the source organism, then gives the criteria by which this sequence is
distinguished from the remainder of the source genome, such as the
gene name and what it codes for, or the protein name and mRNA, or some
description of the sequence's function (if the sequence is
non-coding). If the sequence has a coding region, the description may
be followed by a completeness qualifier, such as cds (complete coding
sequence). There is no limit on the number of lines that may be part
of the DEFINITION. The last line must end with a period.
3.4.5.1 DEFINITION Format for NLM Entries
The DEFINITION line for entries derived from journal-scanning at the NLM is
an automatically generated descriptive summary that accompanies each DNA and
protein sequence. It contains information derived from fields in a database
that summarize the most important attributes of the sequence. The DEFINITION
lines are designed to supplement the accession number and the sequence itself
as a means of uniquely and completely specifying DNA and protein sequences. The
following are examples of NLM DEFINITION lines:
NADP-specific isocitrate dehydrogenase [swine, mRNA, 1 gene, 1585 nt]
94 kda fiber cell beaded-filament structural protein [rats, lens, mRNA
Partial, 1 gene, 1873 nt]
inhibin alpha {promoter and exons} [mice, Genomic, 1 gene, 1102 nt, segment
1 of 2]
cefEF, cefG=acetyl coenzyme A:deacetylcephalosporin C o-acetyltransferase
[Acremonium chrysogenum, Genomic, 2 genes, 2639 nt]
myogenic factor 3, qmf3=helix-loop-helix protein [Japanese quails,
embryo, Peptide Partial, 246 aa]
The first part of the definition line contains information describing
the genes and proteins represented by the molecular sequences. This can
be gene locus names, protein names and descriptions that replace or augment
actual names. Gene and gene product are linked by "=". Any special
identifying terms are presented within brackets, such as: {promoter},
{N-terminal}, {EC 2.13.2.4}, {alternatively spliced}, or {3' region}.
The second part of the definition line is delimited by square brackets, '[]',
and provides details about the molecule type and length. The biological
source, i.e., genus and species or common name as cited by the author.
Developmental stage, tissue type and strain are included if available.
The molecule types include: Genomic, mRNA, Peptide. and Other Genomic
Material. Genomic molecules are assumed to be partial sequence unless
"Complete" is specified, whereas mRNA and peptide molecules are assumed
to be complete unless "Partial" is noted.
3.4.6 ACCESSION Format
This field contains a series of six-character and/or eight-character
identifiers called 'accession numbers'. The six-character accession
number format consists of a single uppercase letter, followed by 5 digits.
The eight-character accession number format consists of two uppercase
letters, followed by 6 digits. The 'primary', or first, of the accession
numbers occupies positions 13 to 18 (6-character format) or positions
13 to 20 (8-character format). Subsequent 'secondary' accession numbers
(if present) are separated from the primary, and from each other, by a
single space. In some cases, multiple lines of secondary accession
numbers might be present, starting at position 13.
The primary accession number of a GenBank entry provides a stable identifier
for the biological object that the entry represents. Accessions do not change
when the underlying sequence data or associated features change.
Secondary accession numbers arise for a number of reasons. For example, a
single accession number may initially be assigned to a sequence described in
a publication. If it is later discovered that the sequence must be entered
into the database as multiple entries, each entry would receive a new primary
accession number, and the original accession number would appear as a secondary
accession number on each of the new entries.
3.4.7 VERSION Format
This line contains two types of identifiers for a GenBank database entry:
a compound accession number and an NCBI GI identifier.
LOCUS AF181452 1294 bp DNA PLN 12-OCT-1999
DEFINITION Hordeum vulgare dehydrin (Dhn2) gene, complete cds.
ACCESSION AF181452
VERSION AF181452.1 GI:6017929
^^^^^^^^^^ ^^^^^^^^^^
Compound NCBI GI
Accession Identifier
Number
A compound accession number consists of two parts: a stable, unchanging
primary-accession number portion (see Section 3.4.6 for a description of
accession numbers), and a sequentially increasing numeric version number.
The accession and version numbers are separated by a period. The initial
version number assigned to a new sequence is one. Compound accessions are
often referred to as "Accession.Version" .
An accession number allows one to retrieve the same biological object in the
database, regardless of any changes that are made to the entry over time. But
those changes can include changes to the sequence data itself, which is of
fundamental importance to many database users. So a numeric version number is
associated with the sequence data in every database entry. If an entry (for
example, AF181452) undergoes two sequence changes, its compound accession
number on the VERSION line would start as AF181452.1 . After the first sequence
change this would become: AF181452.2 . And after the second change: AF181452.3 .
The NCBI GI identifier of the VERSION line also serves as a method for
identifying the sequence data that has existed for a database entry over
time. GI identifiers are numeric values of one or more digits. Since they
are integer keys, they are less human-friendly than the Accession.Version
system described above. Returning to our example for AF181452, it was
initially assigned GI 6017929. If the sequence changes, a new integer GI will
be assigned, perhaps 7345003 . And after the second sequence change, perhaps
the GI would become 10456892 .
Why are both these methods for identifying the version of the sequence
associated with a database entry in use? For two reasons:
- Some data sources processed by NCBI for incorporation into its Entrez
sequence retrieval system do not version their own sequences.
- GIs provide a uniform, integer identifier system for every sequence
NCBI has processed. Some products and systems derived from (or reliant
upon) NCBI products and services prefer to use these integer identifiers
because they can all be processed in the same manner.
GenBank Releases contain only the most recent versions of all sequences
in the database. However, older versions can be obtained via GI-based or
Accession.Version-based queries with NCBI's web-Entrez and network-Entrez
applications. A sequence revision history web page is also available:
http://www.ncbi.nlm.nih.gov/htbin-post/Entrez/girevhist
NOTE: All the version numbers for the compound Accession.Version identifier
system were initialized to a value of one in February 1999, when that
system was introduced.
3.4.8 KEYWORDS Format
The KEYWORDS field does not appear in unannotated entries, but is
required in all annotated entries. Keywords are separated by
semicolons; a "keyword" may be a single word or a phrase consisting of
several words. Each line in the keywords field ends in a semicolon;
the last line ends with a period. If no keywords are included in the
entry, the KEYWORDS record contains only a period.
3.4.9 SEGMENT Format
The SEGMENT keyword is used when two (or more) entries of known
relative orientation are separated by a short (<10 kb) stretch of DNA.
It is limited to one line of the form `n of m', where `n' is the
segment number of the current entry and `m' is the total number of
segments.
3.4.10 SOURCE Format
The SOURCE field consists of two parts. The first part is found after
the SOURCE keyword and contains free-format information including an
abbreviated form of the organism name followed by a molecule type;
multiple lines are allowed, but the last line must end with a period.
The second part consists of information found after the ORGANISM
subkeyword. The formal scientific name for the source organism (genus
and species, where appropriate) is found on the same line as ORGANISM.
The records following the ORGANISM line list the taxonomic
classification levels, separated by semicolons and ending with a
period.
3.4.11 REFERENCE Format
The REFERENCE field consists of five parts: the keyword REFERENCE, and
the subkeywords AUTHORS, TITLE (optional), JOURNAL, MEDLINE (optional),
PUBMED (optional), and REMARK (optional).
The REFERENCE line contains the number of the particular reference and
(in parentheses) the range of bases in the sequence entry reported in
this citation. Additional prose notes may also be found within the
parentheses. The numbering of the references does not reflect
publication dates or priorities.
The AUTHORS line lists the authors in the order in which they appear
in the cited article. Last names are separated from initials by a
comma (no space); there is no comma before the final `and'. The list
of authors ends with a period. The TITLE line is an optional field,
although it appears in the majority of entries. It does not appear in
unpublished sequence data entries that have been deposited directly
into the GenBank data bank, the EMBL Nucleotide Sequence Data Library,
or the DNA Data Bank of Japan. The TITLE field does not end with a
period.
The JOURNAL line gives the appropriate literature citation for the
sequence in the entry. The word `Unpublished' will appear after the
JOURNAL subkeyword if the data did not appear in the scientific
literature, but was directly deposited into the data bank. For
published sequences the JOURNAL line gives the Thesis, Journal, or
Book citation, including the year of publication, the specific
citation, or In press.
The MEDLINE line provides the National Library of Medicine's Medline
unique identifier for a citation (if known). Medline UIs are 8 digit
numbers.
The PUBMED line provides the PubMed unique identifier for a citation
(if known). PUBMED ids are numeric, and are record identifiers for article
abstracts in the PubMed database :
http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed
Citations in PubMed that do not fall within Medline's scope will have only
a PUBMED identifier. Similarly, citations that *are* in Medline's scope but
which have not yet been assigned Medline UIs will have only a PUBMED identifier.
If a citation is present in both the PubMed and Medline databases, both a
MEDLINE and a PUBMED line will be present.
The REMARK line is a textual comment that specifies the relevance
of the citation to the entry.
3.4.12 FEATURES Format
GenBank releases use a feature table format designed jointly by
GenBank, the EMBL Nucleotide Sequence Data Library, and the DNA Data
Bank of Japan. This format is in use by all three databases. The
most complete and accurate Feature Table documentation can be found
on the Web at:
http://www.ncbi.nlm.nih.gov/collab/FT/index.html
Any discrepancy between the abbreviated feature table description
of these release notes and the complete documentation on the Web
should be resolved in favor of the version at the above URL.
The Feature Table specification is also available as a printed
document: `The DDBJ/EMBL/GenBank Feature Table: Definition'. Contact
GenBank at the address shown on the first page of these Release Notes
if you would like a copy.
The feature table contains information about genes and gene products,
as well as regions of biological significance reported in the
sequence. The feature table contains information on regions of the
sequence that code for proteins and RNA molecules. It also enumerates
differences between different reports of the same sequence, and
provides cross-references to other data collections, as described in
more detail below.
The first line of the feature table is a header that includes the
keyword `FEATURES' and the column header `Location/Qualifier.' Each
feature consists of a descriptor line containing a feature key and a
location (see sections below for details). If the location does not
fit on this line, a continuation line may follow. If further
information about the feature is required, one or more lines
containing feature qualifiers may follow the descriptor line.
The feature key begins in column 6 and may be no more than 15
characters in length. The location begins in column 22. Feature
qualifiers begin on subsequent lines at column 22. Location,
qualifier, and continuation lines may extend from column 22 to 80.
Feature tables are required, due to the mandatory presence of the
source feature. The sections below provide a brief introduction to
the feature table format.
3.4.12.1 Feature Key Names
The first column of the feature descriptor line contains the feature
key. It starts at column 6 and can continue to column 20. The list of
valid feature keys is shown below.
Remember, the most definitive documentation for the feature table can
be found at:
http://www.ncbi.nlm.nih.gov/collab/FT/index.html
allele Obsolete; see variation feature key
attenuator Sequence related to transcription termination
C_region Span of the C immunological feature
CAAT_signal `CAAT box' in eukaryotic promoters
CDS Sequence coding for amino acids in protein (includes
stop codon)
conflict Independent sequence determinations differ
D-loop Displacement loop
D_segment Span of the D immunological feature
enhancer Cis-acting enhancer of promoter function
exon Region that codes for part of spliced mRNA
gene Region that defines a functional gene, possibly
including upstream (promotor, enhancer, etc)
and downstream control elements, and for which
a name has been assigned.
GC_signal `GC box' in eukaryotic promoters
iDNA Intervening DNA eliminated by recombination
intron Transcribed region excised by mRNA splicing
J_region Span of the J immunological feature
LTR Long terminal repeat
mat_peptide Mature peptide coding region (does not include stop codon)
misc_binding Miscellaneous binding site
misc_difference Miscellaneous difference feature
misc_feature Region of biological significance that cannot be described
by any other feature
misc_recomb Miscellaneous recombination feature
misc_RNA Miscellaneous transcript feature not defined by other RNA keys
misc_signal Miscellaneous signal
misc_structure Miscellaneous DNA or RNA structure
modified_base The indicated base is a modified nucleotide
mRNA Messenger RNA
mutation Obsolete: see variation feature key
N_region Span of the N immunological feature
old_sequence Presented sequence revises a previous version
polyA_signal Signal for cleavage & polyadenylation
polyA_site Site at which polyadenine is added to mRNA
precursor_RNA Any RNA species that is not yet the mature RNA product
prim_transcript Primary (unprocessed) transcript
primer Primer binding region used with PCR
primer_bind Non-covalent primer binding site
promoter A region involved in transcription initiation
protein_bind Non-covalent protein binding site on DNA or RNA
RBS Ribosome binding site
rep_origin Replication origin for duplex DNA
repeat_region Sequence containing repeated subsequences
repeat_unit One repeated unit of a repeat_region
rRNA Ribosomal RNA
S_region Span of the S immunological feature
satellite Satellite repeated sequence
scRNA Small cytoplasmic RNA
sig_peptide Signal peptide coding region
snRNA Small nuclear RNA
source Biological source of the sequence data represented by
a GenBank record. Mandatory feature, one or more per record.
For organisms that have been incorporated within the
NCBI taxonomy database, an associated /db_xref="taxon:NNNN"
qualifier will be present (where NNNNN is the numeric
identifier assigned to the organism within the NCBI taxonomy
database).
stem_loop Hair-pin loop structure in DNA or RNA
STS Sequence Tagged Site; operationally unique sequence that
identifies the combination of primer spans used in a PCR assay
TATA_signal `TATA box' in eukaryotic promoters
terminator Sequence causing transcription termination
transit_peptide Transit peptide coding region
transposon Transposable element (TN)
tRNA Transfer RNA
unsure Authors are unsure about the sequence in this region
V_region Span of the V immunological feature
variation A related population contains stable mutation
- (hyphen) Placeholder
-10_signal `Pribnow box' in prokaryotic promoters
-35_signal `-35 box' in prokaryotic promoters
3'clip 3'-most region of a precursor transcript removed in processing
3'UTR 3' untranslated region (trailer)
5'clip 5'-most region of a precursor transcript removed in processing
5'UTR 5' untranslated region (leader)
3.4.12.2 Feature Location
The second column of the feature descriptor line designates the
location of the feature in the sequence. The location descriptor
begins at position 22. Several conventions are used to indicate
sequence location.
Base numbers in location descriptors refer to numbering in the entry,
which is not necessarily the same as the numbering scheme used in the
published report. The first base in the presented sequence is numbered
base 1. Sequences are presented in the 5 to 3 direction.
Location descriptors can be one of the following:
1. A single base;
2. A contiguous span of bases;
3. A site between two bases;
4. A single base chosen from a range of bases;
5. A single base chosen from among two or more specified bases;
6. A joining of sequence spans;
7. A reference to an entry other than the one to which the feature
belongs (i.e., a remote entry), followed by a location descriptor
referring to the remote sequence;
A site between two residues, such as an endonuclease cleavage site, is
indicated by listing the two bases separated by a carat (e.g., 23^24).
A single residue chosen from a range of residues is indicated by the
number of the first and last bases in the range separated by a single
period (e.g., 23.79). The symbols < and > indicate that the end point
of the range is beyond the specified base number.
A contiguous span of bases is indicated by the number of the first and
last bases in the range separated by two periods (e.g., 23..79). The
symbols < and > indicate that the end point of the range is beyond the
specified base number. Starting and ending positions can be indicated
by base number or by one of the operators described below.
Operators are prefixes that specify what must be done to the indicated
sequence to locate the feature. The following are the operators
available, along with their most common format and a description.
complement (location): The feature is complementary to the location
indicated. Complementary strands are read 5 to 3.
join (location, location, .. location): The indicated elements should
be placed end to end to form one contiguous sequence.
order (location, location, .. location): The elements are found in the
specified order in the 5 to 3 direction, but nothing is implied about
the rationality of joining them.
3.4.12.3 Feature Qualifiers
Qualifiers provide additional information about features. They take
the form of a slash (/) followed by a qualifier name and, if
applicable, an equal sign (=) and a qualifier value. Feature
qualifiers begin at column 22.
Qualifiers convey many types of information. Their values can,
therefore, take several forms:
1. Free text;
2. Controlled vocabulary or enumerated values;
3. Citations or reference numbers;
4. Sequences;
5. Feature labels.
Text qualifier values must be enclosed in double quotation marks. The
text can consist of any printable characters (ASCII values 32-126
decimal). If the text string includes double quotation marks, each set
must be `escaped' by placing a double quotation mark in front of it
(e.g., /note="This is an example of ""escaped"" quotation marks").
Some qualifiers require values selected from a limited set of choices.
For example, the `/direction' qualifier has only three values `left,'
`right,' or `both.' These are called controlled vocabulary qualifier
values. Controlled qualifier values are not case sensitive; they can
be entered in any combination of upper- and lowercase without changing
their meaning.
Citation or published reference numbers for the entry should be
enclosed in square brackets ([]) to distinguish them from other
numbers.
A literal sequence of bases (e.g., "atgcatt") should be enclosed in
quotation marks. Literal sequences are distinguished from free text by
context. Qualifiers that take free text as their values do not take
literal sequences, and vice versa.
The `/label=' qualifier takes a feature label as its qualifier.
Although feature labels are optional, they allow unambiguous
references to the feature. The feature label identifies a feature
within an entry; when combined with the accession number and the name
of the data bank from which it came, it is a unique tag for that
feature. Feature labels must be unique within an entry, but can be the
same as a feature label in another entry. Feature labels are not case
sensitive; they can be entered in any combination of upper-and
lowercase without changing their meaning.
The following is a partial list of feature qualifiers.
/anticodon Location of the anticodon of tRNA and the amino acid
for which it codes
/bound_moiety Moiety bound
/citation Reference to a citation providing the claim of or
evidence for a feature
/codon Specifies a codon that is different from any found in the
reference genetic code
/codon_start Indicates the first base of the first complete codon
in a CDS (as 1 or 2 or 3)
/cons_splice Identifies intron splice sites that do not conform to
the 5'-GT... AG-3' splice site consensus
/db_xref A database cross-reference; pointer to related information
in another database. A description of all cross-references
can be found at:
http://www.ncbi.nlm.nih.gov/collab/db_xref.html
/direction Direction of DNA replication
/EC_number Enzyme Commission number for the enzyme product of the
sequence
/evidence Value indicating the nature of supporting evidence
/frequency Frequency of the occurrence of a feature
/function Function attributed to a sequence
/gene Symbol of the gene corresponding to a sequence region (usable
with all features)
/label A label used to permanently identify a feature
/map Map position of the feature in free-format text
/mod_base Abbreviation for a modified nucleotide base
/note Any comment or additional information
/number A number indicating the order of genetic elements
(e.g., exons or introns) in the 5 to 3 direction
/organism Name of the organism that is the source of the
sequence data in the record.
/partial Differentiates between complete regions and partial ones
/phenotype Phenotype conferred by the feature
/product Name of a product encoded by a coding region (CDS)
feature
/pseudo Indicates that this feature is a non-functional
version of the element named by the feature key
/rpt_family Type of repeated sequence; Alu or Kpn, for example
/rpt_type Organization of repeated sequence
/rpt_unit Identity of repeat unit that constitutes a repeat_region
/standard_name Accepted standard name for this feature
/transl_except Translational exception: single codon, the translation
of which does not conform to the reference genetic code
/translation Amino acid translation of a coding region
/type Name of a strain if different from that in the SOURCE field
/usedin Indicates that feature is used in a compound feature
in another entry
3.4.12.4 Cross-Reference Information
One type of information in the feature table lists cross-references to
the annual compilation of transfer RNA sequences in Nucleic Acids
Research, which has kindly been sent to us on CD-ROM by Dr. Sprinzl.
Each tRNA entry of the feature table contains a /note= qualifier that
includes a reference such as `(NAR: 1234)' to identify code 1234 in
the NAR compilation. When such a cross-reference appears in an entry
that contains a gene coding for a transfer RNA molecule, it refers to
the code in the tRNA gene compilation. Similar cross-references in
entries containing mature transfer RNA sequences refer to the
companion compilation of tRNA sequences published by D.H. Gauss and M.
Sprinzl in Nucleic Acids Research.
3.4.12.5 Feature Table Examples
In the first example a number of key names, feature locations, and
qualifiers are illustrated, taken from different sequences. The first
table entry is a coding region consisting of a simple span of bases
and including a /gene qualifier. In the second table entry, an NAR
cross-reference is given (see the previous section for a discussion of
these cross-references). The third and fourth table entries use the
symbols `<`and `>' to indicate that the beginning or end of the
feature is beyond the range of the presented sequence. In the fifth
table entry, the symbol `^' indicates that the feature is between
bases.
1 10 20 30 40 50 60 70 79
---------+---------+---------+---------+---------+---------+---------+---------
CDS 5..1261
/product="alpha-1-antitrypsin precursor"
/map="14q32.1"
/gene="PI"
tRNA 1..87
/note="Leu-tRNA-CAA (NAR: 1057)"
/anticodon=(pos:35..37,aa:Leu)
mRNA 1..>66
/note="alpha-1-acid glycoprotein mRNA"
transposon <1..267
/note="insertion element IS5"
misc_recomb 105^106
/note="B.subtilis DNA end/IS5 DNA start"
conflict 258
/replace="t"
/citation=[2]
---------+---------+---------+---------+---------+---------+---------+---------
1 10 20 30 40 50 60 70 79
Example 10. Feature Table Entries
The next example shows the representation for a CDS that spans more
than one entry.
1 10 20 30 40 50 60 70 79
---------+---------+---------+---------+---------+---------+---------+---------
LOCUS HUMPGAMM1 3688 bp ds-DNA PRI 15-OCT-1990
DEFINITION Human phosphoglycerate mutase (muscle specific isozyme) (PGAM-M)
gene, 5' end.
ACCESSION M55673 M25818 M27095
KEYWORDS phosphoglycerate mutase.
SEGMENT 1 of 2
.
.
.
FEATURES Location/Qualifiers
CAAT_signal 1751..1755
/gene="PGAM-M"
TATA_signal 1791..1799
/gene="PGAM-M"
exon 1820..2274
/number=1
/EC_number="5.4.2.1"
/gene="PGAM-M"
intron 2275..2377
/number=1
/gene="PGAM2"
exon 2378..2558
/number=2
/gene="PGAM-M"
.
.
.
//
LOCUS HUMPGAMM2 677 bp ds-DNA PRI 15-OCT-1990
DEFINITION Human phosphoglycerate mutase (muscle specific isozyme) (PGAM-M),
exon 3.
ACCESSION M55674 M25818 M27096
KEYWORDS phosphoglycerate mutase.
SEGMENT 2 of 2
.
.
.
FEATURES Location/Qualifiers
exon 255..457
/number=3
/gene="PGAM-M"
intron order(M55673:2559..>3688,<1..254)
/number=2
/gene="PGAM-M"
mRNA join(M55673:1820..2274,M55673:2378..2558,255..457)
/gene="PGAM-M"
CDS join(M55673:1861..2274,M55673:2378..2558,255..421)
/note="muscle-specific isozyme"
/gene="PGAM2"
/product="phosphoglycerate mutase"
/codon_start=1
/translation="MATHRLVMVRHGESTWNQENRFCGWFDAELSEKGTEEAKRGAKA
IKDAKMEFDICYTSVLKRAIRTLWAILDGTDQMWLPVVRTWRLNERHYGGLTGLNKAE
TAAKHGEEQVKIWRRSFDIPPPPMDEKHPYYNSISKERRYAGLKPGELPTCESLKDTI
ARALPFWNEEIVPQIKAGKRVLIAAHGNSLRGIVKHLEGMSDQAIMELNLPTGIPIVY
ELNKELKPTKPMQFLGDEETVRKAMEAVAAQGKAK"
.
.
.
//
---------+---------+---------+---------+---------+---------+---------+---------
1 10 20 30 40 50 60 70 79
Example 11. Joining Sequences
3.4.13 ORIGIN Format
The ORIGIN record may be left blank, may appear as `Unreported.' or
may give a local pointer to the sequence start, usually involving an
experimentally determined restriction cleavage site or the genetic
locus (if available). The ORIGIN record ends in a period if it
contains data, but does not include the period if the record is left
empty (in contrast to the KEYWORDS field which contains a period
rather than being left blank).
3.4.14 SEQUENCE Format
The nucleotide sequence for an entry is found in the records following
the ORIGIN record. The sequence is reported in the 5 to 3 direction.
There are sixty bases per record, listed in groups of ten bases
followed by a blank, starting at position 11 of each record. The
number of the first nucleotide in the record is given in columns 4 to
9 (right justified) of the record.
4. ALTERNATE RELEASES
NCBI is supplying sequence data in the GenBank flat file format to
maintain compatibility with existing software which require that
particular format. Although we have made every effort to ensure
that these data are presented in the traditional flat file format,
if you encounter any problems in using these data with software which
is based upon the flat file format, please contact us at:
[email protected]
The flat file is just one of many possible report formats that can be
generated from the richer representation supported by the ASN.1 form of the
data. Developers of new software tools should consider using the ASN.1 form
directly to take advantage of those features. Documentation and a Software
Developer's Toolkit for ASN.1 are available through NCBI. You may call NCBI
at (301)496-2475, or subscribe to a developers' electronic newsgroup by
sending your name, address, affiliation, and e-mail address to:
[email protected]
The Software Developer's Toolkit and PostScript documentation for UNIX,
VMS, Ultrix, AIX, MacOS, DOS, and Microsoft Windows systems is available
in a compressed UNIX tar file by anonymous ftp from 'ftp.ncbi.nih.gov',
in the toolbox/ncbi_tools directory. The file is 'ncbi.tar.Z'.
5. KNOWN PROBLEMS OF THE GENBANK DATABASE
5.1 Incorrect Gene Symbols in Entries and Index
The /gene qualifier for many GenBank entries contains values other than the
official gene symbol, such as the product or the standard name of the gene. The
gene symbol index (gbgen.idx) is created from the data in the /gene qualifier
and therefore may contain data other than official gene symbols.
6. GENBANK ADMINISTRATION
The National Center for Biotechnology Information (NCBI), National Library
of Medicine, National Institutes of Health, is responsible for the production
and distribution of the NIH GenBank Sequence Database. NCBI distributes
GenBank sequence data by anonymous FTP, e-mail servers and other
network services. For more information, you may contact NCBI at the
e-mail address: [email protected] or by phone: 301-496-2475.
6.1 Registered Trademark Notice
GenBank (R) is a registered trademark of the U.S. Department of Health
and Human Services for the Genetic Sequence Data Bank.
6.2 Citing GenBank
If you have used GenBank in your research, we would appreciate it if
you would include a reference to GenBank in all publications related
to that research.
When citing data in GenBank, it is appropriate to give the sequence
name, primary accession number, and the publication in which the
sequence first appeared. If the data are unpublished, we urge you to
contact the group which submitted the data to GenBank to see if there
is a recent publication or if they have determined any revisions or
extensions of the data.
It is also appropriate to list a reference for GenBank itself. The
following publication, which describes the GenBank database, should
be cited:
Benson D.A., Karsch-Mizrachi I., Lipman D.J., Ostell J., Rapp B.A.,
Wheeler D.L. GenBank. Nucl. Acids Res. 28(1):15-18 (2000)
The following statement is an example of how you may cite GenBank
data. It cites the sequence, its primary accession number, the group
who determined the sequence, and GenBank. The numbers in parentheses
refer to the GenBank citation above and to the REFERENCE in the
GenBank sequence entry.
`We scanned the GenBank (1) database for sequence similarities and
found one sequence (2), GenBank accession number J01016, which showed
significant similarity...'
(1) Benson, D.A. et al. Nucl. Acids Res. 28(1):15-18 (2000)
(2) Nellen, W. and Gallwitz, D. J. Mol. Biol. 159, 1-18 (1982)
6.3 GenBank Distribution Formats and Media
Complete flat file releases of the GenBank database are available via
NCBI's anonymous ftp server:
ftp://ftp.ncbi.nih.gov
Each release is cumulative, incorporating all previous GenBank data.
No retrieval software is provided. GenBank distribution via CD-ROM
ceased as of GenBank Release 106.0 (April, 1998).
Mirrors of the GenBank FTP site at the NCBI are available from the
San Diego Supercomputer Center and the University of Indiana:
ftp://genbank.sdsc.edu/pub
ftp://bio-mirror.net/biomirror/genbank/
6.4 Other Methods of Accessing GenBank Data
Entrez is a molecular biology database system that presents an integrated
view of DNA and protein sequence data, 3D structure data, complete genomes,
and associated MEDLINE entries. The system is produced by the National
Center for Biotechnology Information (NCBI), and is available only via
the Internet (using the Web-Entrez and Network-Entrez applications).
Accessing Entrez is easy: if you have a World Wide Web browser, such as
Netscape or Internet-Explorer, simply point your browser to:
http://www.ncbi.nlm.nih.gov/
The Web version of Entrez has all the capabilities of the network version,
but with the visual style of the World Wide Web. If you prefer the "look and
feel" of Network-Entrez, you may download Network-Entrez from the NCBI's
FTP server:
ftp://ftp.ncbi.nih.gov/
Versions are available for PC/Windows, Macintosh and several Unix variants.
For information about Network-Entrez, Web-Entrez or any other NCBI
services, you may contact NCBI by e-mail at [email protected] or by
phone at 301-496-2475.
6.5 Request for Corrections and Comments
We welcome your suggestions for improvements to GenBank. We are
especially interested to learn of errors or inconsistencies in the
data. BankIt or Sequin can be used to submit revisions to previous
submissions. In addition, suggestions and corrections can be sent by
electronic mail to: [email protected]. Please be certain to
indicate the GenBank release number (e.g., Release 132.0) and the
primary accession number of the entry to which your comments apply; it
is helpful if you also give the entry name and the current contents of
any data field for which you are recommending a change.
6.6 Credits and Acknowledgments
Credits -
GenBank Release Coordination
Mark Cavanaugh
GenBank Submission Coordination
Ilene Mizrachi
GenBank Annotation Staff
Lori Black, Larissa Brown, Larry Chlumsky, Karen Clark, Irene Fang,
Michael Fetchko, Anjanette Johnston, Pierre Ledoux, Richard McVeigh,
Leonie Misquitta, Ilene Mizrachi, DeAnne Olsen Cravaritis,
Chris O'Sullivan, David Rasko, Leigh Riley, Gert Roosen, Susan
Schafer, Suh-suh Wang, Jane Weisemann, Steven Wilhite, and
Linda Yankie
Data Management and Preparation
Vladimir Alekseyev, Serge Bazhin, Anton Butanaev, Mark Cavanaugh,
Hsiu-Chuan Chen, Jonathan Kans, Michael Kimelman, Jim Ostell,
Joel Plotkin, Karl Sirotkin, Vladimir Soussov, Elena Starchenko,
Hanzhen Sun, Tatiana Tatusov, Carolyn Tolstoshev, Jane Weisemann,
Eugene Yaschenko
Database Administration
Helen Epting, Slava Khotomliansky, Tony Stearman
User Support
Nancy Allmang, Medha Bhagwat, Peter Cooper, Susan Dombrowski,
Renata Geer, Dawn Lipshultz, Eugenia Posey-Marcos, Scott McGinnis,
Vyvy Pham, Barbara Rapp, Monica Romiti, Tao Tao, Rose Marie Woodsmall,
David Wheeler
Project Direction
David Lipman
Acknowledgments -
Contractor support for GenBank production and distribution has been
provided by Management Systems Designers, Inc., ComputerCraft Corporation,
and The KEVRIC Company, Inc.
6.7 Disclaimer
The United States Government makes no representations or warranties
regarding the content or accuracy of the information. The United States
Government also makes no representations or warranties of merchantability
or fitness for a particular purpose or that the use of the sequences will
not infringe any patent, copyright, trademark, or other rights. The
United States Government accepts no responsibility for any consequence
of the receipt or use of the information.
For additional information about GenBank releases, please contact
NCBI by e-mail at [email protected], by phone at (301) 496-2475,
or by mail at:
GenBank
National Library of Medicine
Bldg. 38A Rm. 8N-809
8600 Rockville Pike
Bethesda, MD 20894
FAX: (301) 480-9241
