Release Notes For GenBank Release 117
GBREL.TXT Genetic Sequence Data Bank
15 April 2000
NCBI-GenBank Flat File Release 117.0
Distribution Release Notes
6215002 loci, 7376080723 bases, from 6215002 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 info@ncbi.nlm.nih.gov 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 117.0
1.2 Cutoff Date
1.3 Important Changes in Release 117.0
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 117.0
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: gb-sub@ncbi.nlm.nih.gov
Updates and changes to existing GenBank records:
E-MAIL: update@ncbi.nlm.nih.gov
URL for the new GenBank submission tool - BankIt - on the World Wide Web:
http://0-www-ncbi-nlm-nih-gov.brum.beds.ac.uk/
(see Section 1.5 for additional details about submitting data to GenBank.)
*****************************************************************************
GenBank Release 117.0 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, 117.0, incorporates data available to the databases as of
April 25, 2000. 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: query@ncbi.nlm.nih.gov
1.3 Important Changes in Release 117.0
1.3.1 Organizational changes
Due to database growth, the EST division is now being split into fifty-five
pieces.
Due to database growth, the GSS division is now being split into nineteen
pieces.
Due to database growth, the HTG division is now being split into thirty-one
pieces.
Due to database growth, the INV division is now being split into three pieces.
Due to database growth, the VRL division is now being split into two pieces.
1.3.2 Mutation and Allele features discontinued
Agreement was reached at the May 1999 collaborative DDBJ/EMBL/GenBank
meeting that the functionality provided by the variation, mutation, and
allele features can be represented by just a single feature, variation.
With GenBank Release 117.0, all existing mutation and allele features
have been converted to variation; mutation and allele are no longer legal
feature keys.
Reminder: complete Feature Table documentation is available at this URL:
http://0-www-ncbi-nlm-nih-gov.brum.beds.ac.uk/collab/FT/index.html
1.4 Upcoming Changes
1.4.1 New PUBMED linetype for REFERENCEs
Starting with GenBank Release 119.0 in August 2000, a new PUBMED
linetype will be legal for the REFERENCE block of GenBank flatfiles:
LOCUS AF245949 558 bp RNA VRL 30-APR-2000
DEFINITION Hepatitis C virus isolate P11 clone A41 polyprotein precursor,
E1/E2 region, gene, partial cds.
ACCESSION AF245949
VERSION AF245949.1 GI:7670856
....
REFERENCE 1 (bases 1 to 558)
AUTHORS Farci,P., Shimoda,A., Coiana,A., Diaz,G., Peddis,G.,
Melpolder,J.C., Strazzera,A., Chien,D.Y., Munoz,S.J.,
Balestrieri,A., Purcell,R.H. and Alter,H.J.
TITLE The outcome of acute hepatitis C predicted by the evolution of the
viral quasispecies
JOURNAL Science 288 (5464), 339-344 (2000)
MEDLINE 20230065
PUBMED 10764648
The PUBMED identifier is the record identifier for article abstracts
in the PubMed database :
http://0-www-ncbi-nlm-nih-gov.brum.beds.ac.uk/entrez/query.fcgi?db=PubMed
Abstracts in PubMed that do not fall within Medline's scope will have only
a PUBMED identifier. Similarly, abstracts that *are* in Medline's scope but
which have not yet been assigned Medline UIs will have only a PUBMED identifier.
If an abstract is present in both the PubMed and Medline databases, both Medline UI
and PubMed ID will be provided.
1.4.2 New format for GenBank Index files
Starting with GenBank Release 119.0 in August 2000, the format of the
"index" files for releases will change from a tabular, fixed-column
format to a TAB-delimited, line-oriented format. The header information
at the start of index files will no longer be provided.
In general, index file entries consist of a line containing the indexed
term, followed by a table containing LOCUS/DIVISION/ACCESSION triplets.
For example:
GBKEY.IDX Genetic Sequence Data Bank
15 April 2000
NCBI-GenBank Flat File Release 117.0
Keyword Phrase Index
6215002 loci, 7376080723 bases, from 6215002 reported sequences
....
ZONA PELLUCIDA 2 GLYCOPROTEIN
AB000929 ROD AB000929 CATFZP2G MAM D45067 CJZPG2 PRI Y10767
DOGCZP2G MAM D45069 MRZPG2 PRI Y10690 PIGPZP2G MAM D45064
Notice that the "fixed" format is already broken, due to the presence of
eight-character accession numbers. Rather than define a new fixed format
that will break at some point in the future, and at the expense of slightly
larger files, the new index files for the above example will look like so:
ZONA PELLUCIDA 2 GLYCOPROTEIN
AB000929 ROD AB000929
CATFZP2G MAM D45067
CJZPG2 PRI Y10767
DOGCZP2G MAM D45069
MRZPG2 PRI Y10690
PIGPZP2G MAM D45064
A series of LOCUS/DIVISION/ACCESSION triplets, TAB-delimited (and with
a leading TAB), one per line, will follow each indexed value.
Complete details about the changes to the index files will be provided
via the GenBank newsgroup (bionet.molbio.genbank) and future release notes.
1.4.3 STS division will be split into multiple files
The STS GenBank division (gbsts.seq) will soon be split into multiple
files, since its size exceeds 300MB. This is likely to occur by GenBank
Release 118.0 (June 2000). The resulting files for STS will be:
gbsts1.seq and gbsts2.seq .
1.4.4 File-naming convention for ASN.1 data files will be changed.
Starting with GenBank Release 119.0 in August 2000, the filename
convention for the ASN.1 data files used to create GenBank flatfile
releases will be changed. These ASN.1 files can be found at the NCBI
ftp site:
ftp://ncbi.nlm.nih.gov/ncbi-asn1/
The naming convention for these files is currently:
DIV-CODE.aso.Z
For example:
bct1.aso.Z
bct2.aso.Z
This convention will be changed so that the ASN.1 filenames and the
GenBank flatfile names match more closely:
gbDIV-CODE.aso.Z
For example:
gbbct1.aso.Z
gbbct2.aso.Z
1.4.5 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 1999 DDBJ/EMBL/GenBank
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 finalized, 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 and the GenBank newsgroup as they become available.
1.4.6 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.
1.5 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 : gb-sub@ncbi.nlm.nih.gov
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://0-www-ncbi-nlm-nih-gov.brum.beds.ac.uk/
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: info@ncbi.nlm.nih.gov 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 135 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. gbpri5.seq - Primate sequence entries, part 5.
13. gbrod.seq - Rodent sequence entries.
14. gbmam.seq - Other mammalian sequence entries.
15. gbvrt.seq - Other vertebrate sequence entries.
16. gbinv1.seq - Invertebrate sequence entries, part 1.
17. gbinv2.seq - Invertebrate sequence entries, part 2.
18. gbinv3.seq - Invertebrate sequence entries, part 3.
19. gbpln1.seq - Plant sequence entries (including fungi and algae), part 1.
20. gbpln2.seq - Plant sequence entries (including fungi and algae), part 2.
21. gbpln3.seq - Plant sequence entries (including fungi and algae), part 3.
22. gbbct1.seq - Bacterial sequence entries, part 1.
23. gbbct2.seq - Bacterial sequence entries, part 2.
24. gbvrl1.seq - Viral sequence entries, part 1.
25. gbvrl2.seq - Viral sequence entries, part 2.
26. gbphg.seq - Phage sequence entries.
27. gbsyn.seq - Synthetic and chimeric sequence entries.
28. gbuna.seq - Unannotated sequence entries.
29. gbest1.seq - EST (expressed sequence tag) sequence entries, part 1.
30. gbest2.seq - EST (expressed sequence tag) sequence entries, part 2.
31. gbest3.seq - EST (expressed sequence tag) sequence entries, part 3.
32. gbest4.seq - EST (expressed sequence tag) sequence entries, part 4.
33. gbest5.seq - EST (expressed sequence tag) sequence entries, part 5.
34. gbest6.seq - EST (expressed sequence tag) sequence entries, part 6.
35. gbest7.seq - EST (expressed sequence tag) sequence entries, part 7.
36. gbest8.seq - EST (expressed sequence tag) sequence entries, part 8.
37. gbest9.seq - EST (expressed sequence tag) sequence entries, part 9.
38. gbest10.seq - EST (expressed sequence tag) sequence entries, part 10.
39. gbest11.seq - EST (expressed sequence tag) sequence entries, part 11.
40. gbest12.seq - EST (expressed sequence tag) sequence entries, part 12.
41. gbest13.seq - EST (expressed sequence tag) sequence entries, part 13.
42. gbest14.seq - EST (expressed sequence tag) sequence entries, part 14.
43. gbest15.seq - EST (expressed sequence tag) sequence entries, part 15.
44. gbest16.seq - EST (expressed sequence tag) sequence entries, part 16.
45. gbest17.seq - EST (expressed sequence tag) sequence entries, part 17.
46. gbest18.seq - EST (expressed sequence tag) sequence entries, part 18.
47. gbest19.seq - EST (expressed sequence tag) sequence entries, part 19.
48. gbest20.seq - EST (expressed sequence tag) sequence entries, part 20.
49. gbest21.seq - EST (expressed sequence tag) sequence entries, part 21.
50. gbest22.seq - EST (expressed sequence tag) sequence entries, part 22.
51. gbest23.seq - EST (expressed sequence tag) sequence entries, part 23.
52. gbest24.seq - EST (expressed sequence tag) sequence entries, part 24.
53. gbest25.seq - EST (expressed sequence tag) sequence entries, part 25.
54. gbest26.seq - EST (expressed sequence tag) sequence entries, part 26.
55. gbest27.seq - EST (expressed sequence tag) sequence entries, part 27.
56. gbest28.seq - EST (expressed sequence tag) sequence entries, part 28.
57. gbest29.seq - EST (expressed sequence tag) sequence entries, part 29.
58. gbest30.seq - EST (expressed sequence tag) sequence entries, part 30.
59. gbest31.seq - EST (expressed sequence tag) sequence entries, part 31.
60. gbest32.seq - EST (expressed sequence tag) sequence entries, part 32.
61. gbest33.seq - EST (expressed sequence tag) sequence entries, part 33.
62. gbest34.seq - EST (expressed sequence tag) sequence entries, part 34.
63. gbest35.seq - EST (expressed sequence tag) sequence entries, part 35.
64. gbest36.seq - EST (expressed sequence tag) sequence entries, part 36.
65. gbest37.seq - EST (expressed sequence tag) sequence entries, part 37.
66. gbest38.seq - EST (expressed sequence tag) sequence entries, part 38.
67. gbest39.seq - EST (expressed sequence tag) sequence entries, part 39.
68. gbest40.seq - EST (expressed sequence tag) sequence entries, part 40.
69. gbest41.seq - EST (expressed sequence tag) sequence entries, part 41.
70. gbest42.seq - EST (expressed sequence tag) sequence entries, part 42.
71. gbest43.seq - EST (expressed sequence tag) sequence entries, part 43.
72. gbest44.seq - EST (expressed sequence tag) sequence entries, part 44.
73. gbest45.seq - EST (expressed sequence tag) sequence entries, part 45.
74. gbest46.seq - EST (expressed sequence tag) sequence entries, part 46.
75. gbest47.seq - EST (expressed sequence tag) sequence entries, part 47.
76. gbest48.seq - EST (expressed sequence tag) sequence entries, part 48.
77. gbest49.seq - EST (expressed sequence tag) sequence entries, part 49.
78. gbest50.seq - EST (expressed sequence tag) sequence entries, part 50.
79. gbest51.seq - EST (expressed sequence tag) sequence entries, part 51.
80. gbest52.seq - EST (expressed sequence tag) sequence entries, part 52.
81. gbest53.seq - EST (expressed sequence tag) sequence entries, part 53.
82. gbest54.seq - EST (expressed sequence tag) sequence entries, part 54.
83. gbest55.seq - EST (expressed sequence tag) sequence entries, part 55.
84. gbpat.seq - Patent sequence entries.
85. gbsts.seq - STS (sequence tagged site) sequence entries.
86. gbgss1.seq - GSS (genome survey sequence) sequence entries, part 1.
87. gbgss2.seq - GSS (genome survey sequence) sequence entries, part 2.
88. gbgss3.seq - GSS (genome survey sequence) sequence entries, part 3.
89. gbgss4.seq - GSS (genome survey sequence) sequence entries, part 4.
90. gbgss5.seq - GSS (genome survey sequence) sequence entries, part 5.
91. gbgss6.seq - GSS (genome survey sequence) sequence entries, part 6.
92. gbgss7.seq - GSS (genome survey sequence) sequence entries, part 7.
93. gbgss8.seq - GSS (genome survey sequence) sequence entries, part 8.
94. gbgss9.seq - GSS (genome survey sequence) sequence entries, part 9.
95. gbgss10.seq - GSS (genome survey sequence) sequence entries, part 10.
96. gbgss11.seq - GSS (genome survey sequence) sequence entries, part 11.
97. gbgss12.seq - GSS (genome survey sequence) sequence entries, part 12.
98. gbgss13.seq - GSS (genome survey sequence) sequence entries, part 13.
99. gbgss14.seq - GSS (genome survey sequence) sequence entries, part 14.
100.gbgss15.seq - GSS (genome survey sequence) sequence entries, part 15.
101.gbgss16.seq - GSS (genome survey sequence) sequence entries, part 16.
102.gbgss17.seq - GSS (genome survey sequence) sequence entries, part 17.
103.gbgss18.seq - GSS (genome survey sequence) sequence entries, part 18.
104.gbgss19.seq - GSS (genome survey sequence) sequence entries, part 19.
105.gbhtg1.seq - HTGS (high throughput genomic sequencing) sequence entries, part 1.
106.gbhtg2.seq - HTGS (high throughput genomic sequencing) sequence entries, part 2.
107.gbhtg3.seq - HTGS (high throughput genomic sequencing) sequence entries, part 3.
108.gbhtg4.seq - HTGS (high throughput genomic sequencing) sequence entries, part 4.
109.gbhtg5.seq - HTGS (high throughput genomic sequencing) sequence entries, part 5.
110.gbhtg6.seq - HTGS (high throughput genomic sequencing) sequence entries, part 6.
111.gbhtg7.seq - HTGS (high throughput genomic sequencing) sequence entries, part 7.
112.gbhtg8.seq - HTGS (high throughput genomic sequencing) sequence entries, part 8.
113.gbhtg9.seq - HTGS (high throughput genomic sequencing) sequence entries, part 9.
114.gbhtg10.seq - HTGS (high throughput genomic sequencing) sequence entries, part 10.
115.gbhtg11.seq - HTGS (high throughput genomic sequencing) sequence entries, part 11.
116.gbhtg12.seq - HTGS (high throughput genomic sequencing) sequence entries, part 12.
117.gbhtg13.seq - HTGS (high throughput genomic sequencing) sequence entries, part 13.
118.gbhtg14.seq - HTGS (high throughput genomic sequencing) sequence entries, part 14.
119.gbhtg15.seq - HTGS (high throughput genomic sequencing) sequence entries, part 15.
120.gbhtg16.seq - HTGS (high throughput genomic sequencing) sequence entries, part 16.
121.gbhtg17.seq - HTGS (high throughput genomic sequencing) sequence entries, part 17.
122.gbhtg18.seq - HTGS (high throughput genomic sequencing) sequence entries, part 18.
123.gbhtg19.seq - HTGS (high throughput genomic sequencing) sequence entries, part 19.
124.gbhtg20.seq - HTGS (high throughput genomic sequencing) sequence entries, part 20.
125.gbhtg21.seq - HTGS (high throughput genomic sequencing) sequence entries, part 21.
126.gbhtg22.seq - HTGS (high throughput genomic sequencing) sequence entries, part 22.
127.gbhtg23.seq - HTGS (high throughput genomic sequencing) sequence entries, part 23.
128.gbhtg24.seq - HTGS (high throughput genomic sequencing) sequence entries, part 24.
129.gbhtg25.seq - HTGS (high throughput genomic sequencing) sequence entries, part 25.
130.gbhtg26.seq - HTGS (high throughput genomic sequencing) sequence entries, part 26.
131.gbhtg27.seq - HTGS (high throughput genomic sequencing) sequence entries, part 27.
132.gbhtg28.seq - HTGS (high throughput genomic sequencing) sequence entries, part 28.
133.gbhtg29.seq - HTGS (high throughput genomic sequencing) sequence entries, part 29.
134.gbhtg30.seq - HTGS (high throughput genomic sequencing) sequence entries, part 30.
135.gbhtg31.seq - HTGS (high throughput genomic sequencing) sequence entries, part 31.
Three supplemental files provide the accession numbers of GenBank entries
that are new, updated, or deleted since the previous release:
a. gbchg.txt - Entries updated since the previous release.
b. gbdel.txt - Entries deleted since the previous release.
c. gbnew.txt - Entries new since the previous release.
An experimental file called gbcon.seq provides an alternative representation
for complex sequences, such as "segmented sets" and complete-genomes that have
been split into pieces. The GenBank README describes the experimental CON
division of GenBank in more detail:
ftp://ncbi.nlm.nih.gov/genbank/README.genbank
2.2.5 File Sizes
Uncompressed, the Release 117.0 flatfiles require roughly 24684 MB
(sequence files only) or 29031 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 these release notes have been written, these sizes should not be
used to determine file integrity; they are provided as an aid to planning
only.
File Size File Name
240899932 gbacc.idx
3697435312 gbaut.idx
259376285 gbbct1.seq
234148227 gbbct2.seq
2469130 gbchg.txt
7446 gbdel.txt
230064751 gbest1.seq
230688759 gbest10.seq
230689669 gbest11.seq
230689053 gbest12.seq
230689384 gbest13.seq
230688172 gbest14.seq
230689967 gbest15.seq
230689364 gbest16.seq
230688634 gbest17.seq
230688153 gbest18.seq
230690859 gbest19.seq
227004784 gbest2.seq
230690177 gbest20.seq
230688107 gbest21.seq
230689223 gbest22.seq
230687866 gbest23.seq
230690480 gbest24.seq
230689404 gbest25.seq
230689657 gbest26.seq
230687844 gbest27.seq
230690460 gbest28.seq
213545218 gbest29.seq
227697323 gbest3.seq
188184287 gbest30.seq
189286619 gbest31.seq
214479033 gbest32.seq
212487468 gbest33.seq
212904755 gbest34.seq
213945890 gbest35.seq
230687548 gbest36.seq
230688784 gbest37.seq
230688718 gbest38.seq
230689610 gbest39.seq
230690076 gbest4.seq
230690610 gbest40.seq
230689606 gbest41.seq
230688785 gbest42.seq
230690571 gbest43.seq
230688065 gbest44.seq
230687749 gbest45.seq
230688268 gbest46.seq
230688783 gbest47.seq
230688010 gbest48.seq
230690364 gbest49.seq
162224205 gbest5.seq
230689387 gbest50.seq
230688138 gbest51.seq
224728604 gbest52.seq
230690304 gbest53.seq
230689342 gbest54.seq
60131026 gbest55.seq
172709596 gbest6.seq
230689397 gbest7.seq
230689793 gbest8.seq
230690009 gbest9.seq
14687186 gbgen.idx
209716863 gbgss1.seq
209716737 gbgss10.seq
209718858 gbgss11.seq
209718273 gbgss12.seq
209718903 gbgss13.seq
209716972 gbgss14.seq
209717440 gbgss15.seq
209716493 gbgss16.seq
45627316 gbgss17.seq
269324149 gbgss18.seq
53537840 gbgss19.seq
209716397 gbgss2.seq
209717157 gbgss3.seq
209717188 gbgss4.seq
209716418 gbgss5.seq
209717623 gbgss6.seq
209717853 gbgss7.seq
209716847 gbgss8.seq
209716389 gbgss9.seq
229312313 gbhtg1.seq
129588487 gbhtg10.seq
126886604 gbhtg11.seq
199266411 gbhtg12.seq
98574580 gbhtg13.seq
87466506 gbhtg14.seq
93389177 gbhtg15.seq
93985762 gbhtg16.seq
94044922 gbhtg17.seq
133178337 gbhtg18.seq
96460856 gbhtg19.seq
336397594 gbhtg2.seq
127940860 gbhtg20.seq
121101918 gbhtg21.seq
100726257 gbhtg22.seq
132563056 gbhtg23.seq
158175277 gbhtg24.seq
108629441 gbhtg25.seq
115091260 gbhtg26.seq
119684404 gbhtg27.seq
102224976 gbhtg28.seq
99061895 gbhtg29.seq
263870189 gbhtg3.seq
108287223 gbhtg30.seq
60543977 gbhtg31.seq
263859624 gbhtg4.seq
271292129 gbhtg5.seq
195972451 gbhtg6.seq
83503523 gbhtg7.seq
155820112 gbhtg8.seq
76274661 gbhtg9.seq
258786669 gbinv1.seq
297023653 gbinv2.seq
52542727 gbinv3.seq
217149041 gbjou.idx
177258748 gbkey.idx
72029242 gbmam.seq
7173979 gbnew.txt
239108725 gbpat.seq
11069618 gbphg.seq
260672841 gbpln1.seq
266079165 gbpln2.seq
104460231 gbpln3.seq
229141836 gbpri1.seq
320823504 gbpri2.seq
303853803 gbpri3.seq
356281087 gbpri4.seq
100016289 gbpri5.seq
101180 gbrel.txt
222355114 gbrod.seq
497208802 gbsdr.txt
306678232 gbsts.seq
20020813 gbsyn.seq
3029984 gbuna.seq
170862883 gbvrl1.seq
130038050 gbvrl2.seq
123484415 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 43519 99037802
BCT2 35038 88337952
EST1 68584 26473553
EST10 76360 29498696
EST11 74348 28526718
EST12 75741 30249919
EST13 76176 29029016
EST14 75414 29970118
EST15 74219 31339709
EST16 74819 32866360
EST17 78224 31735814
EST18 82173 33823126
EST19 77064 29877946
EST2 74200 28467067
EST20 74411 31909171
EST21 73328 32682284
EST22 72631 30491663
EST23 76564 31615184
EST24 75619 32682663
EST25 74828 33580957
EST26 71359 29047904
EST27 74505 30717751
EST28 92728 43400337
EST29 85896 30985114
EST3 73347 29744927
EST30 67792 17729385
EST31 69708 18143195
EST32 57185 16980442
EST33 43311 10526967
EST34 42785 10850589
EST35 42690 10453759
EST36 69906 30503062
EST37 75890 32873614
EST38 67198 29762214
EST39 72257 31643176
EST4 74268 28273351
EST40 70515 29328486
EST41 81926 33263603
EST42 73836 29330628
EST43 68101 28185700
EST44 70015 31133439
EST45 77627 38478178
EST46 92929 37829189
EST47 112753 40021801
EST48 74991 25687345
EST49 70972 25734340
EST5 47645 15189912
EST50 72575 26464361
EST51 72123 26107174
EST52 76564 25724688
EST53 71912 27089115
EST54 67447 28715246
EST55 23831 7363605
EST6 53711 16836054
EST7 74268 29287448
EST8 75053 30117072
EST9 76998 29945915
GSS1 83820 35093534
GSS10 66080 35653715
GSS11 69708 39173804
GSS12 62109 32343812
GSS13 69385 36307220
GSS14 67347 33949257
GSS15 65553 29402695
GSS16 83301 39790804
GSS17 17708 7636451
GSS18 104171 69296650
GSS19 22267 14548745
GSS2 83093 36612226
GSS3 83849 38963745
GSS4 74192 38294034
GSS5 72160 38473406
GSS6 69545 34738793
GSS7 71915 36090821
GSS8 70657 36230444
GSS9 67982 33633668
HTG1 1104 175235475
HTG10 655 97251327
HTG11 685 94886084
HTG12 1088 150763648
HTG13 478 74342939
HTG14 422 66588354
HTG15 418 71528214
HTG16 429 71494536
HTG17 450 70914350
HTG18 718 100204595
HTG19 483 72664047
HTG2 1535 258229493
HTG20 671 96382437
HTG21 694 89956946
HTG22 536 75929424
HTG23 6843 90044412
HTG24 2607 116476125
HTG25 5014 74880427
HTG26 5546 77707503
HTG27 9892 74234350
HTG28 5230 69522172
HTG29 1616 73234362
HTG3 1206 201437399
HTG30 3153 78628107
HTG31 3077 41462776
HTG4 1422 198203830
HTG5 4442 200814177
HTG6 2032 146364839
HTG7 352 64483077
HTG8 1136 112246107
HTG9 323 57457226
INV1 35517 124113467
INV2 25979 172413522
INV3 2347 32382002
MAM 23799 21350905
PAT 201544 64034109
PHG 1554 4126077
PLN1 48616 114432038
PLN2 45749 115789825
PLN3 13025 54291534
PRI1 50210 102849561
PRI2 28005 186889843
PRI3 24471 181395849
PRI4 17226 233280718
PRI5 2607 71424221
ROD 54862 84650039
STS 113936 50084452
SYN 3737 9177600
UNA 1791 971847
VRL1 51925 47254737
VRL2 39504 32673714
VRT 39622 37027277
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 117.0 (chloroplast and mitochon-
drial sequences not included):
Entries Bases Species
2903476 4725673828 Homo sapiens
1111461 546539451 Mus musculus
147926 480849338 Drosophila melanogaster
106335 199625187 Caenorhabditis elegans
116929 197483805 Arabidopsis thaliana
128895 83799531 Oryza sativa
106745 53696947 Rattus norvegicus
40838 35628426 Giardia intestinalis
67515 34680586 Lycopersicon esculentum
71900 34397394 Danio rerio
18321 32753166 Saccharomyces cerevisiae
71873 31048923 Glycine max
59385 29086655 Zea mays
65567 28230760 Rattus sp.
38410 23277735 Trypanosoma brucei
53484 22549099 Bos taurus
42779 22423378 Fugu rubripes
40296 19262413 Human immunodeficiency virus type 1
5890 18999715 Escherichia coli
10375 17264178 Schizosaccharomyces pombe
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 1982 680338 606
14 Nov 1983 2274029 2427
20 May 1984 3002088 3665
24 Sep 1984 3323270 4135
25 Oct 1984 3368765 4175
26 Nov 1984 3689752 4393
32 May 1985 4211931 4954
36 Sep 1985 5204420 5700
40 Feb 1986 5925429 6642
42 May 1986 6765476 7416
44 Aug 1986 8442357 8823
46 Nov 1986 9615371 9978
48 Feb 1987 10961380 10913
50 May 1987 13048473 12534
52 Aug 1987 14855145 14020
53 Sep 1987 15514776 14584
54 Dec 1987 16752872 15465
55 Mar 1988 19156002 17047
56 Jun 1988 20795279 18226
57 Sep 1988 22019698 19044
57.1 Oct 1988 23800000 20579
58 Dec 1988 24690876 21248
59 Mar 1989 26382491 22479
60 Jun 1989 31808784 26317
61 Sep 1989 34762585 28791
62 Dec 1989 37183950 31229
63 Mar 1990 40127752 33377
64 Jun 1990 42495893 35100
65 Sep 1990 49179285 39533
66 Dec 1990 51306092 41057
67 Mar 1991 55169276 43903
68 Jun 1991 65868799 51418
69 Sep 1991 71947426 55627
70 Dec 1991 77337678 58952
71 Mar 1992 83894652 65100
72 Jun 1992 92160761 71280
73 Sep 1992 101008486 78608
74 Dec 1992 120242234 97084
75 Feb 1993 126212259 106684
76 Apr 1993 129968355 111911
77 Jun 1993 138904393 120134
78 Aug 1993 147215633 131328
79 Oct 1993 157152442 143492
80 Dec 1993 163802597 150744
81 Feb 1994 173261500 162946
82 Apr 1994 180589455 169896
83 Jun 1994 191393939 182753
84 Aug 1994 201815802 196703
85 Oct 1994 217102462 215273
86 Dec 1994 230485928 237775
87 Feb 1995 248499214 269478
88 Apr 1995 286094556 352414
89 Jun 1995 318624568 425211
90 Aug 1995 353713490 492483
91 Oct 1995 384939485 555694
92 Dec 1995 425860958 620765
93 Feb 1996 463758833 685693
94 Apr 1996 499127741 744295
95 Jun 1996 551750920 835487
96 Aug 1996 602072354 920588
97 Oct 1996 651972984 1021211
98 Dec 1996 730552938 1114581
99 Feb 1997 786898138 1192505
100 Apr 1997 842864309 1274747
101 Jun 1997 966993087 1491069
102 Aug 1997 1053474516 1610848
103 Oct 1997 1160300687 1765847
104 Dec 1997 1258290513 1891953
105 Feb 1998 1372368913 2042325
106 Apr 1998 1502542306 2209232
107 Jun 1998 1622041465 2355928
108 Aug 1998 1797137713 2532359
109 Oct 1998 2008761784 2837897
110 Dec 1998 2162067871 3043729
111 Apr 1999 2569578208 3525418
112 Jun 1999 2974791993 4028171
113 Aug 1999 3400237391 4610118
114 Oct 1999 3841163011 4864570
115 Dec 1999 4653932745 5354511
116 Feb 2000 5805414935 5691170
117 Apr 2000 7376080723 6215002
3. FILE FORMATS
The flat file examples included in this section, while not always from the
current release, are usually fairly recent. Any differences compared to the
actual records are the result of updates to the entries involved.
3.1 File Header Information
Each of the 135 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://0-www-ncbi-nlm-nih-gov.brum.beds.ac.uk/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://0-www-ncbi-nlm-nih-gov.brum.beds.ac.uk/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://0-www-ncbi-nlm-nih-gov.brum.beds.ac.uk/collab/FT/index.html
allele Obsolete; see variation feature key
attenuator Sequence related to transcription termination
C_region Span of the C immunological feature
CAAT_signal `CAAT box' in eukaryotic promoters
CDS Sequence coding for amino acids in protein (includes
stop codon)
conflict Independent sequence determinations differ
D-loop Displacement loop
D_segment Span of the D immunological feature
enhancer Cis-acting enhancer of promoter function
exon Region that codes for part of spliced mRNA
gene Region that defines a functional gene, possibly
including upstream (promotor, enhancer, etc)
and downstream control elements, and for which
a name has been assigned.
GC_signal `GC box' in eukaryotic promoters
iDNA Intervening DNA eliminated by recombination
intron Transcribed region excised by mRNA splicing
J_region Span of the J immunological feature
LTR Long terminal repeat
mat_peptide Mature peptide coding region (does not include stop codon)
misc_binding Miscellaneous binding site
misc_difference Miscellaneous difference feature
misc_feature Region of biological significance that cannot be described
by any other feature
misc_recomb Miscellaneous recombination feature
misc_RNA Miscellaneous transcript feature not defined by other RNA keys
misc_signal Miscellaneous signal
misc_structure Miscellaneous DNA or RNA structure
modified_base The indicated base is a modified nucleotide
mRNA Messenger RNA
mutation Obsolete: see variation feature key
N_region Span of the N immunological feature
old_sequence Presented sequence revises a previous version
polyA_signal Signal for cleavage & polyadenylation
polyA_site Site at which polyadenine is added to mRNA
precursor_RNA Any RNA species that is not yet the mature RNA product
prim_transcript Primary (unprocessed) transcript
primer Primer binding region used with PCR
primer_bind Non-covalent primer binding site
promoter A region involved in transcription initiation
protein_bind Non-covalent protein binding site on DNA or RNA
RBS Ribosome binding site
rep_origin Replication origin for duplex DNA
repeat_region Sequence containing repeated subsequences
repeat_unit One repeated unit of a repeat_region
rRNA Ribosomal RNA
S_region Span of the S immunological feature
satellite Satellite repeated sequence
scRNA Small cytoplasmic RNA
sig_peptide Signal peptide coding region
snRNA Small nuclear RNA
source Biological source of the sequence data represented by
a GenBank record. Mandatory feature, one or more per record.
For organisms that have been incorporated within the
NCBI taxonomy database, an associated /db_xref="taxon:NNNN"
qualifier will be present (where NNNNN is the numeric
identifier assigned to the organism within the NCBI taxonomy
database).
stem_loop Hair-pin loop structure in DNA or RNA
STS Sequence Tagged Site; operationally unique sequence that
identifies the combination of primer spans used in a PCR assay
TATA_signal `TATA box' in eukaryotic promoters
terminator Sequence causing transcription termination
transit_peptide Transit peptide coding region
transposon Transposable element (TN)
tRNA Transfer RNA
unsure Authors are unsure about the sequence in this region
V_region Span of the V immunological feature
variation A related population contains stable mutation
- (hyphen) Placeholder
-10_signal `Pribnow box' in prokaryotic promoters
-35_signal `-35 box' in prokaryotic promoters
3'clip 3'-most region of a precursor transcript removed in processing
3'UTR 3' untranslated region (trailer)
5'clip 5'-most region of a precursor transcript removed in processing
5'UTR 5' untranslated region (leader)
3.4.12.2 Feature Location
The second column of the feature descriptor line designates the
location of the feature in the sequence. The location descriptor
begins at position 22. Several conventions are used to indicate
sequence location.
Base numbers in location descriptors refer to numbering in the entry,
which is not necessarily the same as the numbering scheme used in the
published report. The first base in the presented sequence is numbered
base 1. Sequences are presented in the 5 to 3 direction.
Location descriptors can be one of the following:
1. A single base;
2. A contiguous span of bases;
3. A site between two bases;
4. A single base chosen from a range of bases;
5. A single base chosen from among two or more specified bases;
6. A joining of sequence spans;
7. A reference to an entry other than the one to which the feature
belongs (i.e., a remote entry), followed by a location descriptor
referring to the remote sequence;
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://0-www-ncbi-nlm-nih-gov.brum.beds.ac.uk/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:
info@ncbi.nlm.nih.gov
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:
bits-request@ncbi.nlm.nih.gov
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: info@ncbi.nlm.nih.gov or by phone: 301-496-2475.
6.1 Registered Trademark Notice
GenBank (R) is a registered trademark of the U.S. Department of Health
and Human Services for the Genetic Sequence Data Bank.
6.2 Citing GenBank
If you have used GenBank in your research, we would appreciate it if
you would include a reference to GenBank in all publications related
to that research.
When citing data in GenBank, it is appropriate to give the sequence
name, primary accession number, and the publication in which the
sequence first appeared. If the data are unpublished, we urge you to
contact the group which submitted the data to GenBank to see if there
is a recent publication or if they have determined any revisions or
extensions of the data.
It is also appropriate to list a reference for GenBank itself. The
following publication, which describes the GenBank database, should
be cited:
Benson D.A., Karsch-Mizrachi I., Lipman D.J., Ostell J., Rapp B.A.,
Wheeler D.L. GenBank. Nucl. Acids Res. 28(1):15-18 (2000)
The following statement is an example of how you may cite GenBank
data. It cites the sequence, its primary accession number, the group
who determined the sequence, and GenBank. The numbers in parentheses
refer to the GenBank citation above and to the REFERENCE in the
GenBank sequence entry.
`We scanned the GenBank (1) database for sequence similarities and
found one sequence (2), GenBank accession number J01016, which showed
significant similarity...'
(1) Benson, D.A. et al. Nucl. Acids Res. 28(1):15-18 (2000)
(2) Nellen, W. and Gallwitz, D. J. Mol. Biol. 159, 1-18 (1982)
6.3 GenBank Distribution Formats and Media
Complete flat file releases of the GenBank database are available 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://0-www-ncbi-nlm-nih-gov.brum.beds.ac.uk/
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 info@ncbi.nlm.nih.gov 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: update@ncbi.nlm.nih.gov. Please be certain to
indicate the GenBank release number (e.g., Release 117.0) 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
Michael Amiri, John Anderson, Medha Bhagwat, Lori Black,
Larry Chlumsky, Karen Clark, Irene Fang, Michael Fetchko,
Michael Island, Sunil Kaul, Irene Kim, Junga Kim,
Pierre Ledoux, Daniel Lyman, Baishali Maskeri, Jenny McDowell,
Richard McVeigh, Leonie Misquitta, Michael Murphy, Quy Phung,
Lillian Riddick, Leigh Riley, Susan Schafer,
Suh-suh Wang, Jane Weisemann, Steven Wilhite, Sandhya Xirasagar
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 or that the use of the sequences will
not infringe any patent, copyright, trademark, or other rights. The
United States Government accepts no responsibility for any consequence
of the receipt or use of the information.
For additional information about GenBank releases, please contact
NCBI by e-mail at info@ncbi.nlm.nih.gov, 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
