Release Notes For GenBank Release 74
GBREL.TXT Genetic Sequence Data Bank
15 December 1992
NCBI-GenBank Flat File Release 74.0
Distribution CD-ROM Release Notes
97084 loci, 120242234 bases, from 97084 reported sequences
This document describes the data written on NCBI-GenBank flat file
distribution CD-ROMs. The examples used are from the current release. If you
have any questions or comments about the data bank, the distribution CD-ROM,
or this document, please contact NCBI at: [email protected] or at:
NCBI-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 74.0
As of September 30, 1992, the National Center for Biotechnology Information
(NCBI) at the National Library of Medicine (NLM) assumes responsibility for
the GenBank Sequence Data Bank. Previously, GenBank had been produced under
a contract from the National Institute of General Medical Sciences (NIH) to
IntelliGenetics, Inc. Through an Interagency agreement with the Department
of Energy, NCBI will continue to support Los Alamos National Laboratory
(LANL) in the gathering and annotation of direct submission data.
Release 74.0 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.
At the NLM, sequence entries are created by specialized indexers in the
Division of Library Operations. Over 325,000 articles per year from 3400
journals are scanned for sequence data. These records join the direct
submission data stream from LANL and submissions from the European Molecular
Biology Laboratory (EMBL) Datalibrary and the DNA Database of Japan (DDBJ)
for incorporation within a relational database, NCBI-GenBank. 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 Important Changes in Release 74.0
As described in the release notes of NCBI-GenBank 73.1, an additional division
has been created for Expressed Sequence Tag (EST) data (see file 'gbest.seq'),
and the NLM sequence entries that had appeared in data file 'gbnlm.seq' now
appear in their appropriate taxonomic divisions.
Also as of release 74.0, sequence entries that have traditionally appeared in
gborg.seq are now distributed among the other taxonomic divisions. This and
future releases of NCBI-GenBank will no longer include a separate 'gborg.seq'
data file.
1.3 A Special Note About LOCUS names
Because NCBI processes discrete update streams from LANL, DDBJ, and EMBL,
it is difficult to guarantee the uniqueness of LOCUS names among all sequence
entries. With release 74.0, we were unable to resolve 5 duplicate names before
close-of-data:
Division PRI: HUMDNAJ: X62421 and D13388
HUMWT1: X51630 and D13624
Division ROD: MUSLAMC: X14170 and D13181
Division VRT: QULTROPOM4: X54379 and X54280
QULTROPOM5: X54479 and X54281
We have decided to allow the LOCUS name redundancy rather than filter out the
sequences involved.
1.4 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. Both sections are
principally the same information which is contained in the original
GenBank release notes. The fourth section describes other versions
of the data, the fifth section identifies known problems, and the sixth
contains administrative details and ordering information.
2. ORGANIZATION OF CD-ROM FILES
2.1 CD-ROM Formats
The NCBI-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
and ends with a carriage return and a line-feed character.
The data on the CD-ROMs have both uppercase and lowercase characters.
2.2 Files
The NCBI-GenBank flat file release consists of twenty-one files on the
CD-ROM. The list that follows describes each of the files
included in the distribution. In the following sections there are
additional lists indicating the breakdown of files on the various
media and formats.
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. gbest.seq - EST (expressed sequence tag) 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 printed, these sizes should not be
used to determine file integrity. They are provided as an aid to
planning only.
File Size File Name
3837608 gbacc.idx
13863659 gbaut.idx
45808971 gbbct.seq
23148 gbdat.frm
10695253 gbest.seq
1090189 gbgen.idx
28154186 gbinv.seq
4765937 gbjou.idx
5331751 gbkey.idx
12077416 gbmam.seq
3355884 gbphg.seq
42444010 gbpln.seq
59492007 gbpri.seq
72923 gbrel.txt
5723475 gbrna.seq
48785774 gbrod.seq
7767543 gbsdr.txt
3152160 gbsyn.seq
3030164 gbuna.seq
37156182 gbvrl.seq
13846094 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 basepairs
of DNA in each sequence data file.
Division Entries Basepairs
BCT 10807 18859529
EST 7345 2419854
INV 7779 11443238
MAM 3586 4686533
PHG 882 1269085
PLN 10566 18205125
PRI 19858 21485187
RNA 3084 1735245
ROD 15930 17776322
SYN 1356 1100153
UNA 1651 1501856
VRL 9770 14555556
VRT 4470 5204551
3. FILE FORMATS
3.1 File Header Information
Each of the twenty-one 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 NCBI-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 1992
NCBI-GenBank Flat File Release 74.0
Accession Number Index
97084 loci, 120242234 bases, from 97084 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
thirteen groups, one group for each of the thirteen 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, or EST. 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
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
Because the /gene qualifier has not been exclusively used for gene symbols
from genetic databases, the construction of a Gene Symbol cross reference
index requires extensive manual editing. NCBI has chosen to build an index
more like a keyword index for this field, and use both the GenBank /gene
qualifier and the 'Gene.locus' fields from the NCBI internal database as keys.
Querying such an index with a legitimate Gene Symbol will still retrieve all
keys using that symbol so the utility of the Gene Symbol is not lost, however
the additional capability of more general queries is now supported.
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 distribution CD-ROM includes a data submission form in the file
GBDAT.FRM. Due to the large volume of new sequence data, we encourage
authors to complete this form and return it to the address listed on
the form. This will enable data to be entered more quickly into the
data bank.
You can complete the form with any text editor. You can send the
completed form to GenBank on floppy diskette, or electronically via
INTERNET or BITNET (the electronic mail address is: [email protected]).
You can also print the form, fill it in by hand, and send it to the
mailing address given at the beginning of the form.
The second form in this file 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].
If you have an IBM PC or compatible computer, or a Macintosh personal
computer, we request that you use the Authorin program for submitting
sequences to the data bank. See section 6.6 for information about
obtaining the Authorin program at no charge.
3.5 Sequence Entry Files
The distribution CD-ROM contains thirteen 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 3.5.11.1 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 3.5.13.
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.
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.
STANDARD - Lists information about the degree to which the
entry has been annotated and the level of review to which it has been
subjected. Mandatory subkeyword/exactly one record.
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
NCBI-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)
STANDARD full automatic
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)
STANDARD full automatic
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 thirteen 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). The length is limited to three lines and the last line must
end with a period.
3.5.5.1 DEFINITION Format for NLM Entries
The DEFINITION line for NLM entries from journal articles 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 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.
3.5.8 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.
3.5.9 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.
3.5.10 REFERENCE Format
The REFERENCE field consists of five parts: the keyword REFERENCE, and
the subkeywords AUTHORS, TITLE (optional), JOURNAL and STANDARD.
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 STANDARD line contains information about:
The degree to which the entry has been annotated:
`unannotated' for unannotated entries which include citation and
sequence only.
`simple' for unannotated entries which include the organism name and
protein coding regions as well as the citation and sequence.
`full' for fully annotated entries which include all the data items
that were described by the author.
The level of modification and review:
`automatic' for data subjected only to automated (i.e., software) checks.
`staff_entry' for data that passed both automated and annotator checks.
`staff_review' for data that passed previous review levels as well as
a review by senior annotators and/or outside experts.
The format for the STANDARD line is: annotation degree <SPACE> review level
3.5.11 FEATURES Format
GenBank releases use a new feature table format designed jointly by
GenBank, the EMBL Nucleotide Sequence Data Library, and the DNA Data
Bank of Japan. This format is now used by all three data banks.
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 new 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 front page of these Release Notes.
3.5.11.1 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)
3.5.11.2 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.
3.5.11.3 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. Multiple citations are separated by commas (e.g.,
[1],[2],[3]).
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
/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
3.5.11.4 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. See section 3.5.11.6 for an
example.
The feature tables of human entries contain cross-references to the
Genome Data Base (GDB) in Baltimore, MD. GDB includes information on
mapped genes, probes, and restriction fragment length polymorphisms.
Each entry in that data bank contains the official symbol for the gene
or locus. GDB assigns each gene a unique identifier that remains
associated with that gene, regardless of changes in gene names. In
entries that contain sequences for mapped genes a /note= qualifier
includes this identifier placed within single quotes following the
term `/hgml_locus_uid='. The /note qualifier also includes the map
location in single quotes following the term `/map'. The gene symbol
formerly designated `/nomgen=' is contained in the /gene qualifier.
See section 3.5.11.6 for an example.
For more information about the Genome Data Base, contact:
Genome Data Base
1830 East Monument Street
Baltimore, MD 21205
Telephone: (203) 786-5515
3.5.11.5 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 isoyme) (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 isoyme) (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
3.5.12 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).
3.5.13 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 NCBI-GenBank flat file format to
maintain compatibility with existing software which require that
particular format. Although we have taken 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 format is just one of many possible report forms 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 WITH THE GENBANK DATABASE
5.1 Incorrect Gene Symbols in Entries and Index
The /gene qualifier for many GenBank entries contains values other
than the gene symbol, such as the product or the standard name of the
gene. The gene symbol index (gbhgm.idx) is created from the data in
the /gene qualifier and therefore may contain data other than official
gene symbols.
Additional problems with the human gene symbol data in GenBank arise
from the fact that the mechanism for cross-referencing HGML data has
been manual. In addition, the responsibility for maintaining human
gene symbol data has transferred from HGML to the Genome Data Base
(GDB). During this transition period, maintaining gene symbol
information has been difficult.
6. GENBANK ADMINISTRATION
The National Center for Biotechnology Information (NCBI), National
Library of Medicine, National Institutes of Health, has primary
responsibility for the production and distribution of the NIH
GenBank Sequence Database. The NCBI supports the Los Alamos
National Laboratory (LANL) through an Interagency Agreement with
the Department of Energy. LANL is responsible for for gathering
annotating, and organizing sequence data from direct author
submissions. LANL transmits the data to NCBI for distribution.
NCBI incorporates data from LANL, EMBL, DDBJ, and from journal
scanning at NLM for inclusion within the database. NCBI distributes
sequence data by CD-ROM, anonymous FTP, and e-mail servers.
The electronic mail address for NCBI is: [email protected]
(phone: 301-496-2475); the electronic mail address for LANL is:
[email protected] (phone: 505-665-2177).
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:
Burks, C., Cassidy, M., Cinkosky, M.J., Cumella, K.E., Gilna, P.,
Hayden, J.E-D., Keen, G.M., Kelley, T.A., Kelly, M., Kristofferson,
D., and Ryals, J. GenBank. Nucl. Acids Res. 19 (Suppl):2221-2225
(1991)
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) Burks, C. et al. Nucl. Acids Res. 19 (Suppl):2221-2225 (1991)
(2) Nellen, W. and Gallwitz, D. J. Mol. Biol. 159, 1-18 (1982)
6.4 GenBank Distribution Formats and Media
NCBI-GenBank data are available on industry-standard ISO-9660 CD-ROM.
The standard flat file format is included. (Note: the floppy disk
format was discontinued at Rel. 71 and is NOT part of the NCBI CD-ROM.)
6.5 Other CD-ROM Titles
This documentation accompanies the CD-ROM entitled, NCBI-GenBank (Flat
File Format). Each release is a full release incorporating all previous
GenBank data supplemented by new data from direct submissions, NCBI journal
scanning, and EMBL and DDBJ DNA databases. No retrieval software is provided.
NCBI offers two other CD-ROMs. Entrez: Sequences, contains the complete
information from NCBI-GenBank Rel. 74.0 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. Each of the three titles is in ISO 9660
format and is described in greater detail below.
The CD-ROMs are available by subscription through the Government
Printing Office (GPO). U.S. prices are $57 for an annual subscription
to Entrez:Sequences and $47 for the each of the other disks. An annual
subscription will consist of six releases per year. Orders may be
submitted now using the order form on page 3 for annual
subscriptions, which begin September 15, 1992.
CD-ROM was chosen as the primary distribution medium because of its low
cost and large storage capacity. Due to very limited demand for
magnetic tape versions, half-inch tape in VMS Backup format is
being handled by special order through the GPO. Pricing is
approximately $125 per reel. Contact NCBI for details.
Entrez: Sequences
Entrez: Sequences is a CD-ROM containing molecular sequence and
related bibliographic data with retrieval software. The DNA and
protein sequence data is integrated from a variety of sources, including
NCBI=GenBank, EMBL, DDBJ, PIR and SWISS-PROT. The bibliographic database
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 databases. 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.
Entrez: Sequences contains 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 through anonymous FTP from 'ncbi.nlm.nih.gov' in the
'entrez' directory. Executables for several platforms are available on
an unsupported basis.)
NCBI-Sequences (ASN.1)
This title provides the integrated sequence dataset used on the Entrez:
Sequences CD-ROM in the ISO ASN.1 standard data description format.
DNA and protein sequence data is incorporated, non-redundantly, from
NCBI-GenBank, EMBL, DDBJ, 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.
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 Order Form
Order Processing Code: To fax your orders:
* 5274 (202)512-2233
YES, enter my order as follows:
___ subscription(s) to ENTREZ: Sequences on CD-ROM (List ID ENT)
for $57 to USA addresses for one year for 1st class service.
International customers see chart below for prices.
___ subscription(s) to NCBI-GenBank (Flat File) on CD-ROM (List ID NCBIF)
for $47 to USA addresses for one year for 1st class service.
International customers see chart below for prices.
___ subscription(s) to NCBI-Sequences (ASN.1) on CD-ROM (List ID NCBIA)
for $47 to USA addresses for one year for 1st class service.
International customers see chart below for prices.
The total cost of my order is $__________.
___________________________________ Please choose method of payment:
(Company or personal name)
___ Check payable to the
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___________________________________ |_|_|_|_| Credit card expiration date
(City, State, Zip code)
___________________________________ ___________________________________
(Daytime phone including area code) (Authorizing signature)
___________________________________ Mail To: Superintendent of Documents
(Purchase Order No.) P.O. Box 371954
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May we make your name/address
available to other mailers?
Yes ___ No ___
PRICES FOR INTERNATIONAL CUSTOMERS, INCLUDING AIR MAIL SERVICE FOR ONE YEAR
Location Entrez: NCBI NCBI
Sequences GenBank Sequences
Zone 1.............................$79.97........$67.47......$67.47
(South America)
Zone 2.............................$83.29........$70.79......$70.79
(Europe)
Zone 3.............................$86.29........$73.70......$73.70
(Middle East, Africa)
Zone 4.............................$86.65........$74.15......$74.15
(Asia, Pacific, Australia)
Canada.............................$77.17........$64.67......$64.67
Mexico.............................$77.29........$64.79......$64.79
6.6 Request for Direct Submission of Sequence Data
A successful GenBank requires that the data enter the data bank 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 complete, accurate, and timely data. 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 has extended the GenBank contract to
IntelliGenetics, Inc. for a six-month period to continue the
distribution of IBM PC compatible and Macintosh versions of
AUTHORIN. Contact IntelliGenetics by phone at (415) 962-7364 or by
electronic mail: [email protected].
For those who are unable to use the AUTHORIN program, GenBank has a
printed data submission form. This form is now 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 the address [email protected]; direct mail should go to our
postal address in Los Alamos, which is on the data submission form.
6.7 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 74.0) 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.
6.8 Acknowledgments
NCBI acknowledges the contributions of the National Library of
Medicine's Library Operations Divisions and Los Alamos National
Laboratory in creating new sequence entries for NCBI-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
Fu-Sen Hu
Min-Chi Huang
Susan Krist
Maureen Madden
Lillian Riddick
Nancy Sorden
Jane Weisemann
GenBank Database Staff at Los Alamos National Laboratory
David Brown annotation
Michael Cinkosky computational domain leader
David Crowley programmer
Paul Gilna biological domain leader
Carol Harger annotation
Lisa Hollis annotation
Fiona Jordan annotation
Gifford Keen software coordinator
Marianne Luchini annotation
Ada Lujan data flow
Michelle March annotation
Frances Martinez systems maintenance
Mia McLeod annotation
George Reese programmer
David Rider programmer
Saralee Rodarte data flow
Cindy Kent data flow
Doug Sorensen programmer
Christian Skalka annotation
Jolene Schwertzfeger data flow
Robert Sutherland database administrator
Charles Troup programmer
Laurie Tomlinson data flow
6.9 Disclaimer
The United States Government and Los Alamos National Laboratory make
no representations or warranties regarding the content or accuracy of
the information. The United States Government and Los Alamos National
Laboratory also make no representations or warranties of merchantability
or fitness for a particular purpose and accept 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:
NCBI-GenBank
National Library of Medicine
Bldg. 38A Rm. 8N-809
8600 Rockville Pike
Bethesda, MD 20894
FAX: (301) 480-9241
