Bioinformatics, Volume I Data, Sequence Analysis and Evolution

6. The GenBank
Sequence Record
6.1. Definition,
Accession,
and Organism
Managing Sequence Data 13
A GenBank sequence record is most familiarly viewed as a flat
file with the information being presented in specific fields. DDBJ
and GenBank flat files are similar in design. The EMBL flat file
format, however, is different in design but identical in content to
flat files from GenBank and DDBJ.
Here is the top of the GenBank flat file, showing the top seven fields.
LOCUS AF123456 1510 bp mRNA linear VRT
25-JUL-2000
DEFINITION Gallus gallus doublesex and mab-3
related transcription factor 1
(DMRT1) mRNA, partial cds.
ACCESSION AF123456
VERSION AF123456.2 GI:6633795
KEYWORDS .
SOURCE Gallus gallus (chicken)
ORGANISM Gallus gallus
Eukaryota; Metazoa; Chordata;
Craniata; Vertebrata; Euteleostomi;
Archosauria; Aves; Neognathae;
Galliformes; Phasianidae;
Phasianinae; Gallus
The first token of the LOCUS field is the locus name. At present,
this locus name is the same as the accession number, but in the
past, more descriptive names were used. For instance, HUMHBB
is the locus name for the human beta-globin gene in the record
with accession number U01317. With the increase in the number
of redundant sequences over time, the generation of descriptive
locus names was abandoned. Following the locus name is the
length of the sequence, molecule type of the sequence, topology
of the sequence (linear or circular), GenBank taxonomic or
functional division, and date of the last modification. The DEFI-
NITION line gives a brief description of the sequence including
information about the source organism, gene(s), and molecule
information. The ACCESSION is the database-assigned accession
number, which has one of the following formats: two letters
and six digits or one letter and five digits for INSD records;
four letters and eight digits for WGS records; and two letters,
an underscore, and six to eight digits for RefSeq records. The
VERSION line contains the sequence version and the gi, a
unique numerical identifier for that particular sequence. A Gen-
Bank record may or may not have KEYWORDS. Historically,
the KEYWORD field in the GenBank record was used as a summary
of the information present in the record. It was a free text
field and may have contained gene name, protein name, tissue