Release Notes For GenBank Release 92
GBREL.TXT Genetic Sequence Data Bank
15 December 1995
NCBI-GenBank Flat File Release 92.0
Distribution CD-ROM Release Notes
620765 loci, 425860958 bases, from 620765 reported sequences
This document describes the data written on GenBank flat file
distribution CD-ROMs. If you have any questions or comments about the
data bank, the CD-ROM, 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
1. INTRODUCTION
1.1 Release 92.0
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 Data Bank. NCBI handles
all GenBank direct submission data and authors are advised to use the address
below. Submitters are encouraged to use the free Authorin 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 information about BankIt.)
*****************************************************************************
Release 92.0 is a release of sequence data by NCBI in the GenBank flat file
format. It contains a large number of entries produced at the NLM, derived
from scanning the biomedical literature.
GenBank contains sequences submitted directly to the database by authors
as well as entries created at NLM derived from scanning the biomedical
literature. Over 325,000 articles per year from 3400 journals are scanned
for sequence data. They are supplemented by journals in plant and veterinary
sciences through a collaboration with the National Agricultural Library.
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 form of the data is included on
the Entrez: Sequences CD-ROM and is also available, as is the flat file,
by anonymous FTP to 'ncbi.nlm.nih.gov'.
1.2 Cutoff Date
This full release, 92.0, incorporates data available to the databases as
of November 29, 1995. For more recent data, users are advised to download
the update files by anonymous FTP to 'ncbi.nlm.nih.gov' or to search the
updates via the e-mail server. For instructions, send a mail message with the
word 'help' in it to: [email protected]
1.3 Important Changes in Release 92.0
1.3.1 New /db_xref qualifier
A new qualifier, /db_xref, now appears in the GenBank flatfile format. This
new qualifier serves as a vehicle for the linking of DNA sequence records to
other external databases. The format of /db_xref is as follows:
Qualifier: /db_xref="database:identifier"
Definition: database cross-reference: pointer to related
information in another database.
Scope: all feature keys
Value format: "database:identifier" where database is the name
of the database containing related information, and
identifier is the internal identifier of the related
information according to the naming conventions of
the cross-referenced database.
Alphabetic case of the database name is significant. The list of
allowed database names for /db_xref currently includes:
FLYBASE Database of Genetic and molecular data of Drosophila.
example: /db_xref="FLYBASE:FBgn0000024"
GDB Human Genome Database accession numbers.
example: /db_xref="GDB:G00-128-600"
MIM Mendelian Inheritance in Man numbers.
example: /db_xref="MIM:123456"
PID Protein Identifier, issued by International
collaborators. The identifier for this
cross-reference has a descriptive prefix
indicating the originating database:
e: EMBL
g: GenBank
d: DDBJ
example: /db_xref="PID:e123456789"
SGD Saccharomyces Genome Database accession numbers.
example: /db_xref="SGD:L0000470"
SWISS-PROT Swiss-Prot protein database accession numbers.
example: /db_xref="SWISS-PROT:P12345"
The new db_xref qualifier is used for the sequence identifiers that
both Genbank and EMBL are assigning to CDS translations. In GenBank's
case, these identifiers are known as "gi identifiers", and have previously
appeared via /note qualifiers on CDS features:
CDS 54..1382
/note="ribulose-1,5-bisphosphate carboxylase/oxygenase
activase precursor; NCBI gi: 1006835"
In Releases 92.0 and 93.0, the gi identifiers for translations will appear
via both the /note and the /db_xref qualifiers:
CDS 54..1382
/note="ribulose-1,5-bisphosphate carboxylase/oxygenase
activase precursor; NCBI gi: 1006835"
/db_xref="PID:g1006835"
In Releases 94.0 and higher, the gi identifiers will no longer be added to
the /note qualifier:
CDS 54..1382
/note="ribulose-1,5-bisphosphate carboxylase/oxygenase
activase precursor"
/db_xref="PID:g1006835"
The identifiers that EMBL is now assigning to CDS translations currently
appear in the flatfile as:
CDS join(18344..18440,18565..18650,18733..19985,20781..21567,
21873..22008,22446..22819)
/product="B0457.1"
/note="similar to G-protein coupled receptor protein"
/note="PID:e202272"
Starting with Release 92.0, EMBL's protein identifiers for CDS translations
will begin to appear via the /db_xref qualifier:
CDS join(18344..18440,18565..18650,18733..19985,20781..21567,
21873..22008,22446..22819)
/product="B0457.1"
/note="similar to G-protein coupled receptor protein"
/db_xref="PID:e202272"
For releases 92.0 and 93.0, every attempt will be made to present both
the /note and the /db_xref forms of EMBL's PID's. However, synchronization
problems due to differences in EMBL's and GenBank's release cycles may
make this difficult to achieve. Starting with Release 94.0, only the
/db_xref form will be presented.
1.3.2 New NID linetype
GenBank also assigns unique gi identifiers to every nucleic acid sequence.
Currently, these identifiers appear in the COMMENT field:
LOCUS NTU35111 1674 bp mRNA PLN 04-OCT-1995
DEFINITION Nicotiana tabacum rubisco activase precursor (Rca) mRNA, complete
cds.
ACCESSION U35111
...
COMMENT NCBI gi: 1006834
In Releases 92.0 and 93.0, the nucleic acid gi identifiers will appear via
both the COMMENT and a new linetype of the GenBank flatfile format, called
NID (nucleic acid identifier):
LOCUS NTU35111 1674 bp mRNA PLN 04-OCT-1995
DEFINITION Nicotiana tabacum rubisco activase precursor (Rca) mRNA, complete
cds.
ACCESSION U35111
NID g1006834
...
COMMENT NCBI gi: 1006834
In Releases 94.0 and higher, the nucleic acid gi identifiers will no longer
appear in the COMMENT field.
1.4 Upcoming Changes
1.4.1 New accession number format
Currently, accession numbers used by the nucleotide sequence databases
consist of one prefix letter followed by 5 digits. EST projects and
projects to add patent data have accelerated the need to extend the
accession number space. It is projected that the databases will run out
of accession numbers within 8 to 10 months.
* A new form of accession number will be created, defined as an
8-character alphanumeric string, beginning with two upper case
letters and followed only by digits (e.g., SR004562). Leading and
trailing zeros are significant. The letter 'O' will not be used.
* Existing 6-character accession numbers will remain as they are, and will
never be transformed to an 8-character form.
* New accession numbers will not be used before February 1, 1996.
DDBJ/EMBL/GenBank agree to avoid using new accession numbers as long
as possible after that.
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 has
developed AUTHORIN, an easy-to-use program that enables authors to
enter a sequence, annotate it, and submit it to GenBank or any of the
other data banks. NCBI distributes versions of authorin for IBM
PC-compatibles and the Macintosh. Contact NCBI by phone at 301-496-2475
or by electronic mail: [email protected]
GenBank users may now also use the World Wide Web (WWW) for submitting
sequences to GenBank. A new submission tool - BankIt - provides a simple
forms approach for submitting your sequence and descriptive information to
GenBank. Your submission will be submitted directly to GenBank and
immediately forwarded for inclusion in the EMBL and DDBJ databases.
BankIt may be used with Netscape clients for Unix, Macs, and PCs, the
Mosaic client for Unix, and the MacWeb client for Macs. You can access BankIt
from GenBank's home page:
http://www.ncbi.nlm.nih.gov/
If you have any questions on using BankIt, please contact the GenBank
support staff at '[email protected]' or at (301) 496-2475.
For those who are unable to use either AUTHORIN or BankIt, GenBank has a
printed data submission form. This form is standardized among
EMBL, DDBJ, GenBank, PIR, MIPS, and JIPID. GenBank also provides a
corresponding computer-readable data submission form that can be used
for electronic mail and floppy disk submissions. The GenBank Data
Submission Form (located in the file GBDAT.FRM) can be used to submit
your sequence and annotations. Electronic mail submissions should go
to: [email protected]. Direct mail should go to:
GenBank Submissions
National Center for Biotechnology Information
Bldg. 38A, Rm 8N-803
8600 Rockville Pike
Bethesda, MD 20894
1.6 Organization of This Document
The second section describes the contents of the CD-ROM files. The third
section illustrates the formats of the CD-ROM files. The fourth section
describes other versions of the data, the fifth section identifies known prob-
lems, and the sixth contains administrative details and ordering information.
2. ORGANIZATION OF CD-ROM FILES
2.1 CD-ROM Format
The GenBank CD-ROM distribution files are available on ISO-9660
compatible CD-ROM. The data are written as ASCII files with variable
length records. Each record corresponds to one line in the data bank;
a carriage return/line feed pair terminate each line.
The data on the CD-ROMs have both uppercase and lowercase characters.
2.2 Files
The GenBank flat file release consists of twenty-four files on the
CD-ROM. 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. gbdat.frm - Forms for submitting sequences or corrections to GenBank.
9. gbpri.seq - Primate sequence entries.
10. gbrod.seq - Rodent sequence entries.
11. gbmam.seq - Other mammalian sequence entries.
12. gbvrt.seq - Other vertebrate sequence entries.
13. gbinv.seq - Invertebrate sequence entries.
14. gbpln.seq - Plant sequence entries (including fungi and algae).
15. gbbct.seq - Bacterial sequence entries.
16. gbrna.seq - Structural RNA sequence entries.
17. gbvrl.seq - Viral sequence entries.
18. gbphg.seq - Phage sequence entries.
19. gbsyn.seq - Synthetic and chimeric sequence entries.
20. gbuna.seq - Unannotated sequence entries.
21. gbest1.seq - EST (expressed sequence tag) sequence entries, part 1.
22. gbest2.seq - EST (expressed sequence tag) sequence entries, part 2.
23. gbpat.seq - patent sequence entries.
24. gbsts.seq - STS (sequence tagged site) sequence entries.
2.2.5 File Sizes
The following table indicates 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
22969802 gbacc.idx
217139731 gbaut.idx
129859242 gbbct.seq
518129984 gbest1.seq
498148951 gbest2.seq
3502585 gbgen.idx
104119830 gbinv.seq
28999348 gbjou.idx
23626051 gbkey.idx
28132512 gbmam.seq
27100934 gbpat.seq
4896183 gbphg.seq
128336429 gbpln.seq
162780026 gbpri.seq
15001 gbrel.txt
10153336 gbrna.seq
97784608 gbrod.seq
50282953 gbsdr.txt
65299674 gbsts.seq
9390789 gbsyn.seq
1332672 gbuna.seq
95371522 gbvrl.seq
35620210 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
BCT 25392 47306782
EST 368060 127593776
INV 17952 46821498
MAM 8456 8835533
PAT 22457 7412799
PHG 1102 1647683
PLN 26433 51134545
PRI 53096 47599902
RNA 5083 2653814
ROD 28034 31534438
STS 24150 7991529
SYN 2135 4089815
UNA 467 415619
VRL 27047 29701796
VRT 10901 11121429
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 92.0 (chloroplast and mitochon-
drial sequences not included):
Entries Bases Species
365804 154817348 Homo sapiens
12897 26801036 Caenorhabditis elegans
7679 19335331 Saccharomyces cerevisiae
21309 18016548 Mus musculus
23815 11408751 Arabidopsis thaliana
7012 9990856 Rattus norvegicus
6186 9676087 Drosophila melanogaster
3391 7892182 Escherichia coli
12411 4831193 Oryza sativa
9955 4359035 Human immunodeficiency virus type 1
2967 3737618 Gallus gallus
2088 3729726 Haemophilus influenzae
2675 2815822 Bos taurus
761 2261066 Bacillus subtilis
1524 2202692 Xenopus laevis
598 2059854 Schizosaccharomyces pombe
1558 1915413 Oryctolagus cuniculus
2109 1728771 Zea mays
1848 1481713 Sus scrofa
1857 1453447 Plasmodium falciparum
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 21 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
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 twenty-four files on the distribution CD-ROM 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. RNA - structural RNA sequences
9. VRL - viral sequences
10. PHG - bacteriophage sequences
11. SYN - synthetic sequences
12. UNA - unannotated sequences
13. EST - EST sequences
14. PAT - patent sequences
15. STS - STS 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.
3.3.1 Accession Number Index File
Accession numbers consist of a single letter followed by five digits.
They provide an unchanging designation for the data with which they
are associated, and we encourage you to cite accession numbers
whenever you refer to data from the data bank. The primary accession
number is the first accession number of an entry. It is unique to that
entry. Citation of that number will enable other investigators to
locate the data no matter what entry name changes or other data bank
reorganizations may occur. The accession numbers, however, carry no
intrinsic information about the data.
In addition to the primary accession number, some entries have
secondary accession numbers. Secondary accession numbers arise for a
number of reasons. For example, a single accession number may
initially be assigned to the sequence in an article. If it is later
discovered that the sequence must be entered into the data bank as
multiple entries, each entry would receive a new primary accession
number; the previous accession number would appear as the secondary
accession number in each entry.
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.
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 GenBank Data Submission Form and Error/Suggestion Report Form
The recommended method for submitting sequence data to GenBank is through
the Authorin program. Copies for the Macintosh or PC are available free of
charge. For further information, contact NCBI at (301) 496-2475 or at
the following e-mail address:
[email protected]
By using Authorin you will be assisting the database in making your
data available as quickly and as efficiently as possible.
If it is not possible to use Authorin, there is a data submission
form in this distribution (GBDAT.FRM) which can be filled out with
a text editor and returned to the database, preferably by e-mail.
Direct submission e-mail address: [email protected]
The second form in the GBDAT.FRM is the GenBank Error/Suggestion Report
Form. It is separated from the Data Submission Form by a form-feed
character (<CTRL>L, ASCII octal value 014, ASCII decimal value 12). We
encourage all users to report any errors to the data bank staff
using this form. Like the GenBank Data Submission Form, it may be
printed and filled in by hand and sent by mail to the address given
at the beginning of the form. It may also be filled out using a text
editor and sent to GenBank by electronic mail at: [email protected]
3.5 Sequence Entry Files
The distribution CD-ROM contains fifteen sequence entry data files, one
for each division of GenBank.
3.5.1 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).
3.5.2 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 5, indicating the nature of an entry
(feature key) in the FEATURES table; these codes are described in
Section 3.5.12.1 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 3.5.4 to 3.5.14.
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.
NID - The unique nucleic acid identifier that has been assigned to
the current version of the sequence data that are associated with
the GenBank entry identified by a given primary accession number.
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.
3.5.3 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
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
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
3.5.4 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 fifteen taxonomic
divisions. Each entry's division is identified by a three-letter code
in positions 53 to 55. See Section 3.3 for the 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)
3.5.5 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.
3.5.5.1 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.
3.5.6 ACCESSION Format
This field contains a series of six-character identifiers (accession
numbers: first character a letter, the remainder digits). The primary
(first) accession number occupies positions 13 to 18; subsequent
accession numbers occupy positions 20 to 25, 27 to 32, 34 to 39, 41 to
46, 48 to 53, 55 to 60, 62 to 67, and 69 to 74. No punctuation occurs
between accession numbers or after the final accession number;
accession numbers are separated only by one space.
3.5.7 NID Format
This field contains the unique nucleic acid sequence identifier that is
assigned by NCBI to the sequence data in a GenBank entry. Nucleic acid
identifiers consist of the letter 'g', followed by one or more digits. This
sequence identifier occupies positions 13 and higher.
While accession numbers allow one to retrieve the same biological entry
in the database, regardless of changes to that record, the nucleic acid
identifier changes every time that the underlying sequence changes. Reasons
for sequence changes include: the removal of vector contamination, re-sequencing
of stretches of ambiguous sequence, and the correction of sequencing errors.
At the NCBI, these nucleic acid sequence identifiers are called "gi"
identifiers. In maintaining GenBank, NCBI generates a new gi if a sequence
has changed, and then creates pointers between the old and new gis. Retrieval
of the particular version of a sequence associated with a gi will always be
possible.
3.5.8 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.
3.5.9 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.
3.5.10 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.
3.5.11 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.
3.5.12 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 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 optional. However, a feature table must include one
header line and at least one feature descriptor line.
The sections below provide a brief introduction to the new feature
table format. For a thorough description of the feature table
format, see the document `The DDBJ/EMBL/GenBank Feature Table:
Definition.' If you would like a copy of this publication, contact
GenBank at the address shown on the first page of these Release Notes.
3.5.12.1 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.
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)
cellular Region of cellular DNA
conflict Independent determinations differ
D-loop Displacement loop
D_region Span of the D immunological feature
enhancer Cis-acting enhancer of promoter function
exon Region that codes for part of spliced mRNA
GC_signal `GC box' in eukaryotic promoters
iDNA Intervening DNA eliminated by recombination
insertion_seq Insertion sequence (IS), a small transposon
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
provirus Proviral sequence
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
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
virion Virion (encapsidated) viral sequence
- (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)
3.5.12.2 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.
replace (location, location): The first location indicated should be
replaced by the sequence from the second location; used for
insertions, deletions, and variants.
3.5.12.3 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 list of valid 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
/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 organism if different from that contained in
the entry's ORGANISM field
/partial Differentiates between complete regions and partial ones
/phenotype Phenotype conferred by the feature
/product Name of a product encoded by the sequence
/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 coding region (automatically
generated)
/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
3.5.12.4 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.
3.5.12.5 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. In the sixth table entry, the replace operator is shown.
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 replace(258..258,"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
3.5.13 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).
3.5.14 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 CD-ROM, 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 data bank, should
be cited:
Benson, D., Boguski, M., Lipman, D.J., and Ostell, J. GenBank.
Nucl. Acids Res. 22(17):3441-3444 (1994)
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 brackets
refer to one of the GenBank citations above and 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. et al. Nucl. Acids Res. 22(17):3441-3444 (1994)
(2) Nellen, W. and Gallwitz, D. J. Mol. Biol. 159, 1-18 (1982)
6.3 GenBank Distribution Formats and Media
GenBank data are available on industry-standard ISO-9660 CD-ROM.
The standard flat file format is included.
This documentation accompanies the three CD-ROM set entitled 'GenBank (Flat
File Format)'. Each release is cumulative, incorporating all previous GenBank
data. No retrieval software is provided.
6.4 Other CD-ROM Titles
NCBI offers two other CD-ROM titles. 'Entrez' contains all
information appearing in GenBank Release 92.0, formatted to operate
with an included retrieval program, Entrez, for Macintosh and
PC-compatible computers running Microsoft Windows (3.1 or later). The
other CD-ROM contains sequences and MEDLINE citations in a standard
data description language format, ASN.1; this title will be
discontinued in June 1995 since the same data files are available on
the 'Entrez' CD-ROM. These titles are in ISO 9660 format and are
described in greater detail below.
The CD-ROMs are available by subscription through the Government
Printing Office (GPO). U.S. prices are $102 for an annual subscription
to Entrez and $66 for the GenBank Flat File. Orders are no longer being
accepted for the ASN.1 title. An annual subscription will consist of
six releases per year. Orders may be submitted using the order form
below for annual subscriptions.
Entrez
Entrez is a four CD-ROM set containing molecular sequence and related
bibliographic data with retrieval software. Sequence data is integrated from a
variety of sources, including GenBank, EMBL, DDBJ, dbEST, GSDB, PIR and
SWISS-PROT. The bibliographic component consists of a sequence-related subset
of MEDLINE. The DNA sequence, protein sequence and bibliographic data are
linked to provide easy traversal among the three components. The retrieval
system allows for traditional keyword searching and uses pre-computed
statistical measures of relatedness to allow queries that will find all
articles or sequences similar to an article or sequence of interest.
The Entrez disks contain retrieval software for the Macintosh and for
PC-compatible systems running Microsoft Windows (3.1 or later). A minimum
of 2 Mbytes of memory is necessary. Documentation consists of a 30-page user's
guide for installation and operating instructions. (Source code for an X11
version of the software for VMS and Unix platforms is available via anonymous
FTP from 'ncbi.nlm.nih.gov' in the 'entrez' directory. Executables for several
platforms are available on an unsupported basis.)
Due to the rapid growth of GenBank and other sequence databases, it is
anticipated that Entrez will continue to expand to four (and more)
disks, making alternative means of access more convenient and
economical. In addition to the CD-ROM, there are two other versions of
Entrez that may be accessed via the Internet: 1) Network Entrez, with a
"look and feel" identical to the CD-ROM version; and 2) Web Entrez, a
version of Entrez that has been adapted for use via the World Wide Web.
For more information on these alternatives, please send an e-mail
message to the address [email protected] or call the NCBI Service
Desk at (301)496-2475.
NCBI-Sequences (ASN.1) (to be discontinued June 1995)
This title provides the integrated sequence dataset used on the Entrez CD-ROMs
in the ISO ASN.1 standard data description format. DNA and protein sequence data
is incorporated, non-redundantly, from GenBank, EMBL, DDBJ, GSDB, Swiss-Prot
and PIR, and is linked to journal citations appearing in MEDLINE. The MEDLINE
subset currently consists of approximately 50,000 citations. Files are
provided which contain the inter-document/sequence linkage information and
indices to the byte offsets of the beginning of sequence and bibliographic
records. No retrieval software is provided. PLEASE NOTE: This title is being
discontinued effective June, 1995. New subscribers are advised to order
Entrez instead, since the data on both CD-ROM titles are identical.
Ordering Information
GPO handles all subscriptions and subscription-related questions. Telephone
orders can be placed at (202) 783-3238. Due to high volume of telephone
ordering, GPO encourages ordering by fax or mail. Quantity discounts of 25% are
available for orders of 100 or more CD-ROMs delivered to a single address.
=================================================================================
Superintendent of Documents CD-ROM Subscription Order Form
Order processing code: To fax your orders:
# 5403 (202)512-2233
|_| YES, enter my order as follows:
___ subscriptions to ENTREZ: Sequences on CD-ROM (ENT)
___ subscriptions to NCBI-GenBank (Flat File) on CD-ROM (NCBIF)
The total cost of my order is For privacy protection, check the box
$__________. Price includes postage below:
and handling and is subject to |_| Do not make my name available to
change. other mailers.
___________________________________ Please choose method of payment:
(Company or personal name)
___ Check Payable to the
___________________________________ Superintendent of Documents
(Additional address/attention line) ___ GPO Deposit Account
|_|_|_|_|_|_|_| - |_|
___________________________________ ___ VISA or MasterCard Account
(Street address)
|_|_|_|_|_|_|_|_|_|_|_|_|_|_|_|_|_|_|_|_|
___________________________________
(City, State, ZIP code) |_|_|_|_| (Credit card expiration date)
___________________________________
(Daytime phone including area code) _________________________________________
(Authorizing signature) 6/93
___________________________________ Mail To: Superintendent of Documents
(Purchase Order No. for pre-approved P.O. Box 371954
"Fill and Bill" customers only) Pittsburgh, PA 15250-7954
To open a fill and bill acct.,your
billing office must complete Fill and
Bill Application Form #3695. To
obtain a fill and bill application
form call (202)512-2268.
One Year Subscription Prices (six issues) Including Delivery
____________________________________________________________________________
Location Entrez: NCBI
Sequences GenBank
United States...............................$102.00.........$66.00
Zone 1 (South America)......................$127.24.........$83.08
Zone 2 (Europe).............................$137.44.........$88.06
Zone 3 (Middle East and Africa).............$146.44.........$92.56
Zone 4 (Asia, the Pacific, Australia).......$147.16.........$93.10
Canada......................................$124.30.........$78.88
Mexico......................................$124.48.........$79.06
U.S. delivery via first class mail. Foreign delivery via air mail.
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. Please use the GenBank Error/Suggestion Report Form, which is
part of this distribution of GenBank (located in the file GBDAT.FRM),
to send your suggestions and corrections by electronic mail to:
[email protected] or to the address on the error/suggestion form.
Please be certain to indicate the GenBank release number (e.g.,
Release 92.0) 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 Acknowledgments
NCBI acknowledges the contributions of the National Library of
Medicine's Library Operations Division in creating new sequence
entries for GenBank. The following people are involved in the
addition of new sequence data from the literature and direct
author submissions:
NLM Library Operations Sequence Indexers
Sally Davidson
Michael Fetchko
Phil Henrich
Fu-Sen Hu
Min-Chi Huang
Maureen Madden
Lillian Riddick
Nancy Sorden
David Towne
ComputerCraft Support Contract at NCBI - Quality Assurance and Keyboarding
Kirsty Bates
Irene Fang
Junga Kim
Izabela Makalowska
Simos Marmaras
Shirley Meyers
Monika Momiyama
Joseph Plante
Suzanna Ryan
Jenny Wang
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 NCBI distributions, 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
