1.1 NCBI s Sequence Identifier Syntax

1.1 NCBI's Sequence Identifier Syntax

The National Center for Biotechnology Information (NCBI) uses the following syntax for its BLAST server. NCBI is part of the National Library of Medicine (NLM) at the National Institutes of Health (NIH). The following (including the table) is NCBI's description. See ftp://ftp.ncbi.nih.gov/blast/db/README for details.

The syntax of sequence header lines used by the NCBI BLAST server depends on the database from which each sequence was obtained. The table below lists the identifiers for the databases from which the sequences were derived.

Database name	Identifier syntax
GenBank	gb|accession|locus
EMBL Data Library	emb|accession|locus
DDBJ, DNA Database of Japan	dbj|accession|locus
NBRF PIR	pir||entry
Protein Research Foundation	prf||name
SWISS-PROT	sp|accession|entry name
Brookhaven Protein Data Bank	pdb|entry|chain
Patents	pat|country|number
GenInfo Backbone Id	bbs|number
General database identifier	gnl|database|identifier
NCBI Reference Sequence	ref|accession|locus
Local Sequence identifier	lcl|identifier

For example, an identifier might be "gb|M73307|AGMA13GT", where the "gb" tag indicates that the identifier refers to a GenBank sequence, "M73307" is its GenBank ACCESSION, and "AGMA13GT" is the GenBank LOCUS.

"gi" identifiers are being assigned by NCBI for all sequences contained within NCBI's sequence databases. This identifier provides a uniform and stable naming convention whereby a specific sequence is assigned its unique gi identifier. If a nucleotide or protein sequence changes, however, a new gi identifier is assigned, even if the accession number of the record remains unchanged. Thus, gi identifiers provide a mechanism for identifying the exact sequence that was used or retrieved in a given search.