Release Notes For GenBank Release 115
GBREL.TXT Genetic Sequence Data Bank
15 December 1999
NCBI-GenBank Flat File Release 115.0
Distribution Release Notes
5354511 loci, 4653932745 bases, from 5354511 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 115.0
1.2 Cutoff Date
1.3 Important Changes in Release 115.0
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 115.0
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 115.0 is a release of sequence data by NCBI in the GenBank
flat file 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. Sequence data is also incorporated from the Genome Sequence Data Base
(GSDB), Santa Fe, NM. 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: ncbi.nlm.nih.gov .
1.2 Cutoff Date
This full release, 115.0, incorporates data available to the databases as of
December 9, 1999. For more recent data, users are advised to:
o Download the GenBank Update files by anonymous FTP to 'ncbi.nlm.nih.gov':
ftp://ncbi.nlm.nih.gov/ncbi-asn1 (ASN.1 format)
ftp://ncbi.nlm.nih.gov/genbank (flatfile format)
o Use the Network-Entrez or Web-Entrez applications to interactively query
the Entrez: Nucleotides database (see Section 6.4 of this document).
o Use the NCBI 'query' email server to search the GenBank Updates. Instructions
regarding the use of the e-mail server can be obtained by sending an email
message with the word 'help' in it to: [email protected]
1.3 Important Changes in Release 115.0
1.3.1 Organizational changes
Due to database growth, the PLN division is now being split into three pieces.
Due to database growth, the EST division is now being split into forty-four
pieces.
Due to database growth, the HTG division is now being split into seven pieces.
Due to database growth, the GSS division is now being split into fifteen pieces.
1.3.2 Removal of obsolete NID linetype and PID /db_xref
When the Accession.Version system was introduced in the Spring of 1999, we
stated via the GenBank newsgroup that the NID and PID linetypes would
eventually be phased out:
"The NID linetype and the PID /db_xref qualifier will eventually be
removed from the GenBank flatfile format, probably by August 1999.
However, the NCBI GI identifiers that they contain will remain
available, via the new VERSION linetype and the new GI /db_xref
qualifier."
This removal of NID/PID has been implemented with GenBank Release
115.0 (December 1999). Excerpts from a GenBank record which illustrates
the format change are appended below.
NCBI "GI" sequence identifiers can still be obtained from GenBank flatfiles
via the VERSION linetype and the GI /db_xref qualifier of CDS features.
Previous GenBank flatfile view of the HUMCCLEC1 segmented set:
LOCUS HUMCCLEC1 17079 bp DNA PRI 04-FEB-1999
DEFINITION Homo sapiens cartilage-derived C-type lectin (CLECSF1) gene, exons
1 and 2.
ACCESSION AF077344 AF077343
NID g3982778
VERSION AF077344.1 GI:3982778
KEYWORDS .
SEGMENT 1 of 2
SOURCE human.
ORGANISM Homo sapiens
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Mammalia;
Eutheria; Primates; Catarrhini; Hominidae; Homo.
REFERENCE 1 (bases 1 to 17079)
AUTHORS Neame,P.J. and Tapp,H.
TITLE The Cartilage-Derived, C-type Lectin (CLECSF1); Structure of the
Human Gene and Chromosomal Location
JOURNAL Unpublished
....
FEATURES Location/Qualifiers
source 1..17079
/organism="Homo sapiens"
/db_xref="taxon:9606"
/chromosome="16"
/map="16q23"
/tissue_type="cartilage"
repeat_region complement(180..393)
/rpt_family="MIR"
....
//
LOCUS HUMCCLEC2 3362 bp DNA PRI 04-FEB-1999
DEFINITION Homo sapiens cartilage-derived C-type lectin (CLECSF1) gene, exon 3
and complete cds.
ACCESSION AF077345
NID g3386489
VERSION AF077345.1 GI:3386489
KEYWORDS .
SEGMENT 2 of 2
SOURCE human.
ORGANISM Homo sapiens
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Mammalia;
Eutheria; Primates; Catarrhini; Hominidae; Homo.
REFERENCE 1 (bases 1 to 3362)
AUTHORS Neame,P.J. and Tapp,H.
TITLE The Cartilage-Derived, C-type Lectin (CLECSF1); Structure of the
Human Gene and Chromosomal Location
JOURNAL Unpublished
....
FEATURES Location/Qualifiers
source 1..3362
/organism="Homo sapiens"
/db_xref="taxon:9606"
/chromosome="16"
/map="16q23"
/tissue_type="cartilage"
mRNA join(AF077344.1:10886..11079,AF077344.1:16446..16529,
777..1171)
/gene="CLECSF1"
/product="cartilage-derived C-type lectin"
gene order(AF077344.1:10886..17079,1..3362)
/gene="CLECSF1"
CDS join(AF077344.1:10965..11079,AF077344.1:16446..16529,
777..1171)
/gene="CLECSF1"
/note="similar to tetranectin"
/codon_start=1
/product="cartilage-derived C-type lectin"
/protein_id="AAD12542.1"
/db_xref="PID:g3386491"
/db_xref="GI:3386491"
/translation="MAKNGLVICILVITLLLDQTTSHTSRLKARKHSKRRVRDKDGDL
KTQIEKLWTEVNALKEIQALQTVCLRGTKVHKKCYLASEGLKHFHEANEDCISKGGIL
VIPRNSDEINALQDYGKRSLPGVNDFWLGINDMVTEGKFVDVNGIAISFLNWDRAQPN
GGKRENCVLFSQSAQGKWSDEACRSSKRYICEFTIPQ"
....
//
GenBank flatfile view of the HUMCCLEC1 segmented set as of December 1999.
Note the lack of the NID linetype and the PID /db_xref :
LOCUS HUMCCLEC1 17079 bp DNA PRI 04-FEB-1999
DEFINITION Homo sapiens cartilage-derived C-type lectin (CLECSF1) gene, exons
1 and 2.
ACCESSION AF077344 AF077343
VERSION AF077344.1 GI:3982778
KEYWORDS .
SEGMENT 1 of 2
SOURCE human.
ORGANISM Homo sapiens
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Mammalia;
Eutheria; Primates; Catarrhini; Hominidae; Homo.
REFERENCE 1 (bases 1 to 17079)
AUTHORS Neame,P.J. and Tapp,H.
TITLE The Cartilage-Derived, C-type Lectin (CLECSF1); Structure of the
Human Gene and Chromosomal Location
JOURNAL Unpublished
....
FEATURES Location/Qualifiers
source 1..17079
/organism="Homo sapiens"
/db_xref="taxon:9606"
/chromosome="16"
/map="16q23"
/tissue_type="cartilage"
repeat_region complement(180..393)
/rpt_family="MIR"
....
//
LOCUS HUMCCLEC2 3362 bp DNA PRI 04-FEB-1999
DEFINITION Homo sapiens cartilage-derived C-type lectin (CLECSF1) gene, exon 3
and complete cds.
ACCESSION AF077345
VERSION AF077345.1 GI:3386489
KEYWORDS .
SEGMENT 2 of 2
SOURCE human.
ORGANISM Homo sapiens
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Mammalia;
Eutheria; Primates; Catarrhini; Hominidae; Homo.
REFERENCE 1 (bases 1 to 3362)
AUTHORS Neame,P.J. and Tapp,H.
TITLE The Cartilage-Derived, C-type Lectin (CLECSF1); Structure of the
Human Gene and Chromosomal Location
JOURNAL Unpublished
....
FEATURES Location/Qualifiers
source 1..3362
/organism="Homo sapiens"
/db_xref="taxon:9606"
/chromosome="16"
/map="16q23"
/tissue_type="cartilage"
mRNA join(AF077344.1:10886..11079,AF077344.1:16446..16529,
777..1171)
/gene="CLECSF1"
/product="cartilage-derived C-type lectin"
gene order(AF077344.1:10886..17079,1..3362)
/gene="CLECSF1"
CDS join(AF077344.1:10965..11079,AF077344.1:16446..16529,
777..1171)
/gene="CLECSF1"
/note="similar to tetranectin"
/codon_start=1
/product="cartilage-derived C-type lectin"
/protein_id="AAD12542.1"
/db_xref="GI:3386491"
/translation="MAKNGLVICILVITLLLDQTTSHTSRLKARKHSKRRVRDKDGDL
KTQIEKLWTEVNALKEIQALQTVCLRGTKVHKKCYLASEGLKHFHEANEDCISKGGIL
VIPRNSDEINALQDYGKRSLPGVNDFWLGINDMVTEGKFVDVNGIAISFLNWDRAQPN
GGKRENCVLFSQSAQGKWSDEACRSSKRYICEFTIPQ"
....
//
1.3.3 Introduction of the "CON" division
A new and experimental file called gbcon.seq is included with GenBank Release 115.0.
This data file contains instructions for the assembly of larger-scale objects (eg,
"contigs", hence the new division's name) from individual GenBank records. It is unusual
in that the records in this file contain no sequence data at all. For an overview of this
experimental GenBank division, please see the following NCBI News article:
http://www.ncbi.nlm.nih.gov/Web/Newsltr/Fall99/contig.html
One class of data represented in gbcon.seq is derived from "segmented sets". Genomic
DNA sequences can sometimes be incomplete because submittors choose to sequence just the
exons, small portions of the intervening introns, and perhaps some upstream or downstream
control regions. These related sequences are labelled "1 of N", "2 of N", etc, via
the SEGMENT line in the GenBank flatfile format. There is often a coding region feature
on the last member, with a join() location pointing to exon intervals that contribute
to the coding sequence. Gaps of unknown size typically exist between the sequenced pieces.
Entries in the new gbcon.seq file make the relationships among such pieces more explicit.
In addition, these entries have accession numbers, version numbers, and NCBI GIs, just like
regular GenBank records. Here's an example illustrating these points:
LOCUS AH007743 7832 bp DNA CON 26-MAY-1999
DEFINITION Gallus gallus ornithine transcarbamylase (OTC) gene, complete cds.
ACCESSION AH007743
VERSION AH007743.1 GI:4927367
KEYWORDS .
SOURCE chicken.
ORGANISM Gallus gallus
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Archosauria;
Aves; Neognathae; Galliformes; Phasianidae; Phasianinae; Gallus.
[....]
FEATURES Location/Qualifiers
source 1..7832
/organism="Gallus gallus"
/db_xref="taxon:9031"
/chromosome="1"
CONTIG join(AF065630.1:1..1903,gap(),AF065631.1:1..435,gap(),
AF065632.1:1..509,gap(),AF065633.1:1..722,gap(),AF065634.1:1..707,
gap(),AF065635.1:1..836,gap(),AF065636.1:1..1614,gap(),
AF065637.1:1..605,gap(),AF065638.1:1..501)
//
The second class of data represented in gbcon.seq results from splitting large complete
genomes (eg, bacterial genomes) into multiple pieces. GenBank has a single-record size
limit of 350,000 bases. Complete genomes larger than this are split (without
interrupting any coding regions), with a small overlap between each piece (about 60 bases
for bacterial genomes). The CON division entries for these genomes provides instructions
for the re-assembly of the complete genome from these separate pieces.
This new GenBank division is experimental, and thus some caveats apply to the new
data file:
o gbcon.seq doesn't have a "header"
o the content of gbcon.seq is not reflected in any of the index files (gb*.idx)
o if all literature references for the members of a segmented set are
associated with an incomplete span of the sequence, no references appear
at all for the gbcon.seq entry
o definition lines for segmented-set CON entries are sometimes less than ideal:
- genus and species only
- the content reflects one member of the segset, not the set as a whole
o some complete bacterial genomes are not yet represented in gbcon.seq due
to ongoing work with complete-genome dataflow
These problems will be addressed in the next two months. In the meantime,
the gbcon.seq data file will give users a chance to experiment with this
new data representation. If problems other than those described above are
encountered, we'd like to hear of them. Please send your problem reports to
the NCBI Service Desk (see Section 6).
1.4 Upcoming Changes
1.4.1 Replacement of organelle-related qualifiers with /organelle
A large variety of organelle qualifiers currently exist: /mitochondrion,
/chromoplast, /chloroplast, etc. Starting with GenBank Release 116.0 (February,
2000), these qualifiers will all be incorporated into a single new qualifier,
with a controlled value format. The preliminary description of this qualifier
is as follows:
Qualifier /organelle=""
Definition type of membrane-bound intracellular structure from
which the sequence was obtained
Value format mitochondrion, nucleomorph, plastid, mitochondrion:kinetoplast,
plastid:chloroplast, plastid:apicoplast, plastid:chromoplast,
plastid:cyanelle, plastid:leucoplast, plastid:proplastid
Examples /organelle="mitochondrion"
/organelle="nucleomorph"
/organelle="plastid"
/organelle="mitochondrion:kinetoplast"
/organelle="plastid:chloroplast"
/organelle="plastid:apicoplast"
/organelle="plastid:chromoplast"
/organelle="plastid:cyanelle"
/organelle="plastid:leucoplast"
/organelle="plastid:proplastid"
Comments modifier text limited to values from controlled list
1.4.2 Mutation and Allele features to be discontinued
Agreement was reached at the May 1999 collaborative DDBJ/EMBL/GenBank
meeting that the functionality provided by the variation, mutation, and
allele features could be represented by just a single feature, variation.
Submittors of sequence data are now being encouraged to use just the
variation feature. With GenBank Release 117.0, all existing mutation and
allele features will be converted to variation, and then mutation and
allele features will no longer be legal feature keys.
1.4.3 New REFERENCE type for on-line journals
Agreement was reached at the May 1999 collaborative DDBJ/EMBL/GenBank
meeting that an effort should be made to accomodate references which are
published only on-line. Until specifications for such references are
available from library organizations, GenBank will present them in a manner
like this:
REFERENCE 1 (bases 1 to 2858)
AUTHORS Smith, J.
TITLE Cloning and expression of a phospholipase gene
JOURNAL Online Publication
REMARK Online-Journal-name; Article Identifier; URL
This format is still tentative; additional information about this new
reference type will be made available via these release notes.
1.4.4 Selenocysteine representation
Selenocysteine residues within the protein translations of coding
region features have been represented in GenBank via the letter 'X'
and a /transl_except qualifier. At the May collaborative meeting, it
was learned that IUPAC plans to adopt the letter 'U' for selenocysteine.
DDBJ, EMBL, and GenBank will thus use this new amino acid abbreviation
for its /translation qualifiers. Although a timetable for its appearance
has not been decided upon, we are mentioning this now because the
introduction of a new residue abbreviation is a fairly fundamental change.
Details about the use of 'U' will be made available via these release
notes as they become available.
1.4.5 VRL division will be split into multiple files
The viral GenBank division (gbvrl.seq) will soon be split into multiple
files, since its size is approaching 300MB. This is likely to occur by
GenBank Release 117.0 (April 2000). The resulting files for VRL will be:
gbvrl1.seq and gbvrl2.seq .
1.5 Request for Direct Submission of Sequence Data
A successful GenBank requires that the 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 ncbi.nlm.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://ncbi.nlm.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 ninety-three files. The list
that follows describes 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. gbaut.idx - Index of the entries according to author.
6. gbjou.idx - Index of the entries according to journal citation.
7. gbgen.idx - Index of the entries according to gene names.
8. gbpri1.seq - Primate sequence entries, part 1.
9. gbpri2.seq - Primate sequence entries, part 2.
10. gbpri3.seq - Primate sequence entries, part 3.
11. gbpri4.seq - Primate sequence entries, part 4.
12. gbrod.seq - Rodent sequence entries.
13. gbmam.seq - Other mammalian sequence entries.
14. gbvrt.seq - Other vertebrate sequence entries.
15. gbinv1.seq - Invertebrate sequence entries, part 1.
16. gbinv2.seq - Invertebrate sequence entries, part 2.
17. gbpln1.seq - Plant sequence entries (including fungi and algae), part 1.
18. gbpln2.seq - Plant sequence entries (including fungi and algae), part 2.
19. gbpln3.seq - Plant sequence entries (including fungi and algae), part 3.
20. gbbct1.seq - Bacterial sequence entries, part 1.
21. gbbct2.seq - Bacterial sequence entries, part 2.
22. gbvrl.seq - Viral sequence entries.
23. gbphg.seq - Phage sequence entries.
24. gbsyn.seq - Synthetic and chimeric sequence entries.
25. gbuna.seq - Unannotated sequence entries.
26. gbest1.seq - EST (expressed sequence tag) sequence entries, part 1.
27. gbest2.seq - EST (expressed sequence tag) sequence entries, part 2.
28. gbest3.seq - EST (expressed sequence tag) sequence entries, part 3.
29. gbest4.seq - EST (expressed sequence tag) sequence entries, part 4.
30. gbest5.seq - EST (expressed sequence tag) sequence entries, part 5.
31. gbest6.seq - EST (expressed sequence tag) sequence entries, part 6.
32. gbest7.seq - EST (expressed sequence tag) sequence entries, part 7.
33. gbest8.seq - EST (expressed sequence tag) sequence entries, part 8.
34. gbest9.seq - EST (expressed sequence tag) sequence entries, part 9.
35. gbest10.seq - EST (expressed sequence tag) sequence entries, part 10.
36. gbest11.seq - EST (expressed sequence tag) sequence entries, part 11.
37. gbest12.seq - EST (expressed sequence tag) sequence entries, part 12.
38. gbest13.seq - EST (expressed sequence tag) sequence entries, part 13.
39. gbest14.seq - EST (expressed sequence tag) sequence entries, part 14.
40. gbest15.seq - EST (expressed sequence tag) sequence entries, part 15.
41. gbest16.seq - EST (expressed sequence tag) sequence entries, part 16.
42. gbest17.seq - EST (expressed sequence tag) sequence entries, part 17.
43. gbest18.seq - EST (expressed sequence tag) sequence entries, part 18.
44. gbest19.seq - EST (expressed sequence tag) sequence entries, part 19.
45. gbest20.seq - EST (expressed sequence tag) sequence entries, part 20.
46. gbest21.seq - EST (expressed sequence tag) sequence entries, part 21.
47. gbest22.seq - EST (expressed sequence tag) sequence entries, part 22.
48. gbest23.seq - EST (expressed sequence tag) sequence entries, part 23.
49. gbest24.seq - EST (expressed sequence tag) sequence entries, part 24.
50. gbest25.seq - EST (expressed sequence tag) sequence entries, part 25.
51. gbest26.seq - EST (expressed sequence tag) sequence entries, part 26.
52. gbest27.seq - EST (expressed sequence tag) sequence entries, part 27.
53. gbest28.seq - EST (expressed sequence tag) sequence entries, part 28.
54. gbest29.seq - EST (expressed sequence tag) sequence entries, part 29.
55. gbest30.seq - EST (expressed sequence tag) sequence entries, part 30.
56. gbest31.seq - EST (expressed sequence tag) sequence entries, part 31.
57. gbest32.seq - EST (expressed sequence tag) sequence entries, part 32.
58. gbest33.seq - EST (expressed sequence tag) sequence entries, part 33.
59. gbest34.seq - EST (expressed sequence tag) sequence entries, part 34.
60. gbest35.seq - EST (expressed sequence tag) sequence entries, part 35.
61. gbest36.seq - EST (expressed sequence tag) sequence entries, part 36.
62. gbest37.seq - EST (expressed sequence tag) sequence entries, part 37.
63. gbest38.seq - EST (expressed sequence tag) sequence entries, part 38.
64. gbest39.seq - EST (expressed sequence tag) sequence entries, part 39.
65. gbest40.seq - EST (expressed sequence tag) sequence entries, part 40.
66. gbest41.seq - EST (expressed sequence tag) sequence entries, part 41.
67. gbest42.seq - EST (expressed sequence tag) sequence entries, part 42.
68. gbest43.seq - EST (expressed sequence tag) sequence entries, part 43.
69. gbest44.seq - EST (expressed sequence tag) sequence entries, part 44.
70. gbpat.seq - Patent sequence entries.
71. gbsts.seq - STS (sequence tagged site) sequence entries.
72. gbgss1.seq - GSS (genome survey sequence) sequence entries, part 1.
73. gbgss2.seq - GSS (genome survey sequence) sequence entries, part 2.
74. gbgss3.seq - GSS (genome survey sequence) sequence entries, part 3.
75. gbgss4.seq - GSS (genome survey sequence) sequence entries, part 4.
76. gbgss5.seq - GSS (genome survey sequence) sequence entries, part 5.
77. gbgss6.seq - GSS (genome survey sequence) sequence entries, part 6.
78. gbgss7.seq - GSS (genome survey sequence) sequence entries, part 7.
79. gbgss8.seq - GSS (genome survey sequence) sequence entries, part 8.
80. gbgss9.seq - GSS (genome survey sequence) sequence entries, part 9.
81. gbgss10.seq - GSS (genome survey sequence) sequence entries, part 10.
82. gbgss11.seq - GSS (genome survey sequence) sequence entries, part 11.
83. gbgss12.seq - GSS (genome survey sequence) sequence entries, part 12.
84. gbgss13.seq - GSS (genome survey sequence) sequence entries, part 13.
85. gbgss14.seq - GSS (genome survey sequence) sequence entries, part 14.
86. gbgss15.seq - GSS (genome survey sequence) sequence entries, part 15.
87. gbhtg1.seq - HTGS (high throughput genomic sequencing) sequence entries, part 1.
88. gbhtg2.seq - HTGS (high throughput genomic sequencing) sequence entries, part 2.
89. gbhtg3.seq - HTGS (high throughput genomic sequencing) sequence entries, part 3.
90. gbhtg4.seq - HTGS (high throughput genomic sequencing) sequence entries, part 4.
91. gbhtg5.seq - HTGS (high throughput genomic sequencing) sequence entries, part 5.
92. gbhtg6.seq - HTGS (high throughput genomic sequencing) sequence entries, part 6.
93. gbhtg7.seq - HTGS (high throughput genomic sequencing) sequence entries, part 7.
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.
2.2.5 File Sizes
Uncompressed, the Release 115.0 flatfiles require roughly 18917 MB
(sequence files only) or 22026 MB (including the 'index' files). The
following table contains the approximate sizes of the individual files
in this release. Since minor changes to some of the files may occur
after the release notes are written, these sizes should not be used to
determine file integrity; they are provided as an aid to planning only.
File Size File Name
207316201 gbacc.idx
2120416703 gbaut.idx
255042336 gbbct1.seq
178758501 gbbct2.seq
224729062 gbest1.seq
225894489 gbest10.seq
242128531 gbest11.seq
183184497 gbest12.seq
164722601 gbest13.seq
231115305 gbest14.seq
252489233 gbest15.seq
256447580 gbest16.seq
253183448 gbest17.seq
246868558 gbest18.seq
257708603 gbest19.seq
233243448 gbest2.seq
262309048 gbest20.seq
263017649 gbest21.seq
262744096 gbest22.seq
262470007 gbest23.seq
263674782 gbest24.seq
263891184 gbest25.seq
265409687 gbest26.seq
253621936 gbest27.seq
253494030 gbest28.seq
254930860 gbest29.seq
240203921 gbest3.seq
231749961 gbest30.seq
243520088 gbest31.seq
239233763 gbest32.seq
203606848 gbest33.seq
212401636 gbest34.seq
251697269 gbest35.seq
251990057 gbest36.seq
260169381 gbest37.seq
261923548 gbest38.seq
242889635 gbest39.seq
241324285 gbest4.seq
222258957 gbest40.seq
214213922 gbest41.seq
216642055 gbest42.seq
218679219 gbest43.seq
238589462 gbest44.seq
239027808 gbest5.seq
238287530 gbest6.seq
240868860 gbest7.seq
234635839 gbest8.seq
229740242 gbest9.seq
12714301 gbgen.idx
269134964 gbgss1.seq
224165283 gbgss10.seq
233706596 gbgss11.seq
237552083 gbgss12.seq
230684274 gbgss13.seq
235828788 gbgss14.seq
227938649 gbgss15.seq
51639091 gbgss2.seq
228257663 gbgss3.seq
225874636 gbgss4.seq
224936910 gbgss5.seq
233405449 gbgss6.seq
65970937 gbgss7.seq
223281769 gbgss8.seq
222744427 gbgss9.seq
216047614 gbhtg1.seq
286778651 gbhtg2.seq
270605920 gbhtg3.seq
243330077 gbhtg4.seq
262104642 gbhtg5.seq
239215723 gbhtg6.seq
130890552 gbhtg7.seq
254972865 gbinv1.seq
124822887 gbinv2.seq
187760916 gbjou.idx
151977389 gbkey.idx
66365419 gbmam.seq
218763195 gbpat.seq
10238346 gbphg.seq
254925903 gbpln1.seq
269443405 gbpln2.seq
5476987 gbpln3.seq
169884688 gbpri1.seq
257002049 gbpri2.seq
354847742 gbpri3.seq
311914264 gbpri4.seq
102961 gbrel.txt
204454734 gbrod.seq
428366503 gbsdr.txt
246313628 gbsts.seq
18715212 gbsyn.seq
1187213 gbuna.seq
270314801 gbvrl.seq
109020012 gbvrt.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 44457 97593292
BCT2 24813 68580180
EST1 93291 29075498
EST2 76326 26498687
EST3 75698 27839242
EST4 77714 27720193
EST5 78010 28461525
EST6 77610 27916718
EST7 71553 30428455
EST8 73365 27620442
EST9 79067 28626376
EST10 71146 29130126
EST11 77007 29481644
EST12 54628 18893105
EST13 50298 14388071
EST14 73642 28648281
EST15 81774 31882944
EST16 97729 36312402
EST17 88102 34509488
EST18 79879 31237261
EST19 84491 33921827
EST20 88871 34733990
EST21 91965 36244694
EST22 88933 36318853
EST23 84798 37022614
EST24 95972 40133250
EST25 92562 37879451
EST26 90794 38445308
EST27 76413 31681802
EST28 80538 36588099
EST29 81567 32891419
EST30 80128 29925192
EST31 87116 30872222
EST32 81800 32843559
EST33 72024 22527042
EST34 72435 23538976
EST35 82576 32867533
EST36 91243 35778927
EST37 83264 36592760
EST38 87274 38604419
EST39 62537 26522644
EST40 50175 15684393
EST41 44738 11161002
EST42 44797 12788030
EST43 46334 12540558
EST44 74740 32545793
GSS1 104169 69190682
GSS2 21390 14226352
GSS3 91502 43233839
GSS4 77178 41157207
GSS5 78356 43155351
GSS6 72395 38364588
GSS7 22857 12155090
GSS8 89724 37628643
GSS9 88808 39053719
GSS10 87069 41478701
GSS11 81615 42661259
GSS12 84208 43675797
GSS13 83029 41541260
GSS14 82156 41958067
GSS15 77685 38688584
HTG1 1095 167058539
HTG2 1605 219161023
HTG3 2222 200231302
HTG4 1300 182870143
HTG5 3517 193560635
HTG6 1491 177533870
HTG7 1542 98523743
INV1 35052 122793344
INV2 19912 62884897
MAM 22020 19619171
PAT 185865 57516823
PHG 1488 3793050
PLN1 48712 109796680
PLN2 46590 119611340
PLN3 780 2595651
PRI1 50660 57079417
PRI2 27732 148522465
PRI3 16266 228967162
PRI4 15209 203821419
ROD 51454 76587881
STS 92407 33619956
SYN 3548 8568823
UNA 484 327104
VRL 82001 72474398
VRT 35224 32746483
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 115.0 (chloroplast and mitochon-
drial sequences not included):
Entries Bases Species
2701438 2668877955 Homo sapiens
926626 383506676 Mus musculus
144672 304857076 Drosophila melanogaster
106053 193236061 Caenorhabditis elegans
97820 152791472 Arabidopsis thaliana
122918 70629565 Oryza sativa
82764 43702473 Rattus norvegicus
18263 32738646 Saccharomyces cerevisiae
65559 28221599 Rattus sp.
54348 27764180 Lycopersicon esculentum
56548 26927994 Danio rerio
47139 23407791 Zea mays
42778 22505243 Fugu rubripes
5385 18721272 Escherichia coli
35768 16677558 Human immunodeficiency virus type 1
10287 16249181 Schizosaccharomyces pombe
24424 15215793 Trypanosoma brucei
5595 12350174 Plasmodium falciparum
1110 10074140 Bacillus subtilis
20115 9584918 Dictyostelium discoideum
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.
Over the period 1982 to the present, the number of bases in GenBank
has doubled approximately every 14 months.
Release Date Base Pairs Entries
3 Dec 82 680338 606
14 Nov 83 2274029 2427
20 May 84 3002088 3665
24 Sep 84 3323270 4135
25 Oct 84 3368765 4175
26 Nov 84 3689752 4393
32 May 85 4211931 4954
36 Sep 85 5204420 5700
40 Feb 86 5925429 6642
42 May 86 6765476 7416
44 Aug 86 8442357 8823
46 Nov 86 9615371 9978
48 Feb 87 10961380 10913
50 May 87 13048473 12534
52 Aug 87 14855145 14020
53 Sep 87 15514776 14584
54 Dec 87 16752872 15465
55 Mar 88 19156002 17047
56 Jun 88 20795279 18226
57 Sep 88 22019698 19044
57.1 Oct 88 23800000 20579
58 Dec 88 24690876 21248
59 Mar 89 26382491 22479
60 Jun 89 31808784 26317
61 Sep 89 34762585 28791
62 Dec 89 37183950 31229
63 Mar 90 40127752 33377
64 Jun 90 42495893 35100
65 Sep 90 49179285 39533
66 Dec 90 51306092 41057
67 Mar 91 55169276 43903
68 Jun 91 65868799 51418
69 Sep 91 71947426 55627
70 Dec 91 77337678 58952
71 Mar 92 83894652 65100
72 Jun 92 92160761 71280
73 Sep 92 101008486 78608
74 Dec 92 120242234 97084
75 Feb 93 126212259 106684
76 Apr 93 129968355 111911
77 Jun 93 138904393 120134
78 Aug 93 147215633 131328
79 Oct 93 157152442 143492
80 Dec 93 163802597 150744
81 Feb 94 173261500 162946
82 Apr 94 180589455 169896
83 Jun 94 191393939 182753
84 Aug 94 201815802 196703
85 Oct 94 217102462 215273
86 Dec 94 230485928 237775
87 Feb 95 248499214 269478
88 Apr 95 286094556 352414
89 Jun 95 318624568 425211
90 Aug 95 353713490 492483
91 Oct 95 384939485 555694
92 Dec 95 425860958 620765
93 Feb 96 463758833 685693
94 Apr 96 499127741 744295
95 Jun 96 551750920 835487
96 Aug 96 602072354 920588
97 Oct 96 651972984 1021211
98 Dec 96 730552938 1114581
99 Feb 97 786898138 1192505
100 Apr 97 842864309 1274747
101 Jun 97 966993087 1491069
102 Aug 97 1053474516 1610848
103 Oct 97 1160300687 1765847
104 Dec 97 1258290513 1891953
105 Feb 98 1372368913 2042325
106 Apr 98 1502542306 2209232
107 Jun 98 1622041465 2355928
108 Aug 98 1797137713 2532359
109 Oct 98 2008761784 2837897
110 Dec 98 2162067871 3043729
111 Apr 99 2569578208 3525418
112 Jun 99 2974791993 4028171
113 Aug 99 3400237391 4610118
114 Oct 99 3841163011 4864570
115 Dec 99 4653932745 5354511
3. FILE FORMATS
The flat file examples included in this section, while not always from the
current release, are usually quite recent. Any differences compared to the
actual data files are the result of updates to the entries involved.
3.1 File Header Information
Each of the ninety-three 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 data bank name (Genetic Sequence Data Bank) starting in
column 20. 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 26. The fourth line contains
the current GenBank release number. The release number appears in
positions 41 to 45 and consists of two 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 7, the number of bases in positions 15 to 23, and the
number of reports in positions 37 to 40. (There are more reports of
sequences than entries since reported sequences that overlap or
duplicate each other are combined into single entries.) The third,
fifth, seventh, and ninth lines are blank.
1 10 20 30 40 50 60 70 79
---------+---------+---------+---------+---------+---------+---------+---------
GBACC.IDX Genetic Sequence Data Bank
15 December 1993
GenBank Flat File Release 80.0
Accession Number Index
150744 loci, 163802597 bases, from 150744 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 five files containing indices to the entries in this release:
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. (The index keys
for the keyword phrases and author names appear in uppercase
characters even though they appear in mixed case in the sequence
entries.) Under each index key, the names of the sequence entries
containing that index key are listed alphabetically. Each sequence
name is also followed by its data file division and primary accession
number. The following codes are used to designate the data file
divisions:
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)
The index key begins in column 1 of a record. An 11-character field
for the sequence entry name starts in position 14 of a record,
followed by a 3-character field for the data file division, starting
at position 25 and ending at position 27, and a 6-character field for
the primary accession number, starting at position 29 and ending at
position 34. All entries in the fields are left-justified.
Beginning at positions 36 and 58, the three fields repeat, so three
sets of sequence information can appear in one record. If there are
more than three entry names, the next records are used; the index key
is not repeated. For the accession number files, the entry names begin
in the same record as the index key, since the key is always less than
12 characters. In the other index files, the entry names begin on the
record following the index key record.
NOTE: The column positions stated above will be shifted to the
right if primary accessions in the 8-character format are present.
3.3.1 Accession Number Index File
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).
The following excerpt from the accession number index file illustrates
the format of the index:
1 10 20 30 40 50 60 70 79
---------+---------+---------+---------+---------+---------+---------+---------
J00316 HUMTBB11P PRI J00316
J00317 HUMTBB46P PRI J00317
J00318 HUMUG1 PRI J00318
J00319 HUMUG1PA PRI J00319
J00320 HUMVIPMR1 PRI L00154 HUMVIPMR2 PRI L00155 HUMVIPMR3 PRI L00156
HUMVIPMR4 PRI L00157 HUMVIPMR5 PRI L00158
J00321 BABA1AT PRI J00321
J00322 CHPRSA PRI J00322
J00323 AGMRSASPC PRI J00323
J00324 BABATIII PRI J00324
---------+---------+---------+---------+---------+---------+---------+---------
1 10 20 30 40 50 60 70 79
Example 4. Accession Number Index File
If the same accession number is found in more than one entry (a result
of the infrequent occasions when a single entry is split into two or
more separate entries), then the additional entries and groups in
which the number appears are also given. In the example above, J00320
is a secondary accession, appearing on 5 other database entries.
3.3.2 Keyword Phrase Index File
Keyword phrases consist of names for gene products and other
characteristics of sequence entries. There are approximately 18,000
keyword phrases. An excerpt from the keyword phrase index file is
shown below:
1 10 20 30 40 50 60 70 79
---------+---------+---------+---------+---------+---------+---------+---------
DNA HELICASE
ECOHELIV BCT J04726 ECOUVRD BCT X00738 FPLTRAX BCT M38047
HS2ULL VRL D10470 HSECOMGEN VRL M86664 PT4DDA PHG M93048
SYNPMMB190 SYN M37846 YSPRHP3 PLN X64583
DNA HELICASE I
ECOPTRAI5 BCT X57430
DNA HELICASE II
ECOUVRD2 BCT D00069 HEAMUTB1A BCT M99049
DNA INVERSION SYSTEM
ECOP15BG BCT X62121
DNA INVERTASE
ECOPIN BCT K00676 ECOPIN1 BCT X01805 PMUGINMOM PHG V01463
STABINR3 BCT X16298 STAINVSA BCT M36694
DNA J HEATSHOCK PROTEIN
MSGDNAJHSP BCT M95576
DNA LIGASE
ECOLIG BCT M24278 ECOLIGA BCT M30255 PT4G30 PHG X00039
PT6LIG55 PHG M38465 TTHDNALGS BCT M74792 TTHDNALIG BCT M36417
VACCDNLIG VRL X16512 VACRHF VRL D11079 YSCCDC9 PLN X03246
YSPCDC17 PLN X05107 ZMOLIG BCT Z11910
---------+---------+---------+---------+---------+---------+---------+---------
1 10 20 30 40 50 60 70 79
Example 5. Keyword Phrase Index File
3.3.3 Author Name Index File
The author name index file lists all of the author names that appear
in the citations. An excerpt from the author name index file is shown
below:
1 10 20 30 40 50 60 70 79
---------+---------+---------+---------+---------+---------+---------+---------
JACKSON,D.I.
RATLCAG1 ROD M18349 RATLCAG2 ROD M18348 RATLCAG3 ROD M18347
RATLCAI ROD M25820 RATLCAII ROD M25821 RATLCAIII ROD M25822
RATLCAIV ROD M25823 RATLCAR ROD Y00065
JACKSON,F.R.
DRO16883C INV X62939 DRO1688ED INV X62938 DRO1688EP INV X62937
DROPER INV M11969 DROPES INV X03636 MUSPER ROD M12039
MUSURFPER ROD X02966
JACKSON,I.J.
MUSHOMA ROD X03033 MUSNEORP8R ROD X54812 MUSP7H2 ROD X54811
MUSRPT ROD M69041 MUSSOFI ROD X63350 MUSTRP15 ROD X59513
MUSTYRP2 ROD X63349
JACKSON,I.M.
RATTRH ROD M12138
JACKSON,J.
DROFPS85D INV X52844 MUSIGKAC3 ROD K00885 MUSIL4RA ROD M27959
MUSIL4RB ROD M27960 RABGLOBCON MAM L05833 RABGLOBHSB MAM L05835
---------+---------+---------+---------+---------+---------+---------+---------
1 10 20 30 40 50 60 70 79
Example 6. Author Name Index File
3.3.4 Journal Citation Index File
The journal citation index file lists all of the citations that appear
in the references. All citations are truncated to 80 characters. An
excerpt from the citation index file is shown below:
1 10 20 30 40 50 60 70 79
---------+---------+---------+---------+---------+---------+---------+---------
(IN) THE IMMUNE SYSTEM: 132-138, S. KARGER, NEW YORK (1981)
HUMIGHVX PRI M35415
(IN) THE LENS: TRANSPARANCY AND CATARACT: 171-179, EURAGE, RIJSWIJK (1986)
RANCRYG2A VRT K02264 RANCRYG4A VRT K02266 RANCRYG5A VRT M22529
RANCRYG6A VRT M22530 RANCRYR VRT X00659
(IN) THIOREDOXIN AND GLUTAREDOXIN SYSTEMS: STRUCTURE AND FUNCTION: 11-19, UNKNOW
ECOTRXA1 BCT M54881
(IN) UCLA SYMP. MOL. CELL. BIOL. NEW SER., VOL. 77: 339-352, ALAN R. LISS, INC.
BOVTRNB2A MAM M36431 HUMTRNB PRI M36429 HUMTRNB1 PRI M36430
(IN) UCLA SYMPOSIA: 575-584, ALAN R. LISS, INC., NEW YORK (1987)
PFAHGPRT INV M54896
(IN) VIRUS RESEARCH. PROCEEDINGS OF 1973 ICN-UCLA SYMPOSIUM: 533-544, ACADEMIC
LAMCG PHG J02459
ACTA BIOCHIM. BIOPHYS. SIN. 23, 246-253 (1992)
HUMPLASINS PRI M98056
---------+---------+---------+---------+---------+---------+---------+---------
1 10 20 30 40 50 60 70 79
Example 7. Journal Citation Index File
3.3.5 Gene Name Index
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. An excerpt from the gene name
index file is shown below:
1 10 20 30 40 50 60 70 79
---------+---------+---------+---------+---------+---------+---------+---------
SUPPRESSOR OF SABLE
DROSUSG INV M57889
SUPPRESSOR TWO OF ZESTE
DROS2ZSTG INV X56798
SUPRESSOR TWO OF ZESTE
DROS2ZSTM INV X56799
SUR
CHKSRVCNTK VRT M57290
SURC
ARFSURCG BCT X63435
---------+---------+---------+---------+---------+---------+---------+---------
1 10 20 30 40 50 60 70 79
Example 8. Gene Name Index File
3.4 Sequence Entry Files
GenBank releases contain forty-four 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).
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 four subkeywords and may repeat. Mandatory
keyword/one or more records.
AUTHORS - Lists the authors of the citation. Mandatory
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.
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 pieces of information contained in the LOCUS record are always
found in fixed positions. The locus name (or entry name), which is
always ten 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 29.
The letters `bp' are in positions 31 to 32. Positions 34 to 36 give
the number of strands of the sequence. Positions 37 to 40 give the
topology of molecule sequenced. If the sequence is of a special type,
a notation (such as `circular') is included in positions 43 to 52.
GenBank sequence entries are divided among sixteen different
divisions. Each entry's division is specified by a three-letter code
in positions 53 to 55. See Section 3.3 for an explanation of division
codes.
Positions 63 to 73 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 record is as follows:
Positions Contents
1-12 LOCUS
13-22 Locus name
23-29 Length of sequence, right-justified
31-32 bp
34-36 Blank, ss- (single-stranded), ds- (double-stranded), or
ms- (mixed-stranded)
37-40 Blank, DNA, RNA, tRNA (transfer RNA), rRNA (ribosomal RNA),
mRNA (messenger RNA), or uRNA (small nuclear RNA)
43-52 Blank (implies linear) or circular
53-55 The division code (see Section 3.3)
63-73 Date, in the form dd-MMM-yyyy (e.g., 15-MAR-1991)
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 from 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 the same way.
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
application. 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),
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 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 Related strain contains alternative gene form
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 A mutation alters the sequence here
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;
8. A literal sequence (a string of bases enclosed in quotation marks).
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.
group (location, location, .. location): The elements are related and
should be grouped together, but no order is implied.
one-of (location, location, .. location): The element can be any one,
but only one, of the items listed.
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 'ncbi.nlm.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., Boguski, M.S., Lipman, D.J., Ostell, J.,
Ouellette, B.F.F., Rapp, B.A., and Wheeler, D.L.. GenBank.
Nucl. Acids Res. 27(1):12-17 (1999)
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) data bank 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. 27(1):12-17 (1999)
(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 only via
anonymous ftp from :
ftp://ncbi.nlm.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).
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://ncbi.nlm.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 to [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 115.0) 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
Gabriella Ryan Adams, Michael Amiri, Medha Bhagwat, Lori Black,
Larry Chlumsky, Karen Clark, Irene Fang, Michael Fetchko,
Pamela Jacques, Anthony Jung, Irene Kim, Junga Kim, Jaime Kolonay,
Pierre Ledoux, Daniel Lyman, Baishali Maskeri, Jenny McDowell,
Richard McVeigh, Lillian Riddick, Leigh Riley, Susan Schafer,
Suh-suh Wang, Jane Weisemann, Steven Wilhite, and Linda Yankie
Data Management and Preparation
Serge Bazhin, Mark Cavanaugh, Hsiu-Chuan Chen, Jim Ostell,
Joel Plotkin, Sergei Shavirin, Karl Sirotkin, Vladimir Soussov,
Tatiana Tatusov, Carolyn Tolstoshev, Jane Weisemann,
Database Administration
Cat Lukens, Eugene Yaschenko
Production and User Support
Dennis Benson, Peter Cooper, Jim Fleshman, Susan Kimball,
Renata McCarthy, Scott McGinnis, Monica Romiti, Barbara Rapp,
Steven Rosenthal, 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 and accepts no responsibility for
any consequences 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
