SEQ-Ids Whats in a Name

The accession number was an improvement over the locus/ID name, but, with use, problems and deficiencies became apparent. For example, although the accession 

For these reasons, all internal processing of sequences at NCBI, from computing Entrez sequence neighbors to determining when new sequence should be processed or producing the BLAST databases, is based on gi numbers. 

Recently, the members of the International Nucleotide Sequence Database Collaboration (GenBank, EMBL, and DDBJ) introduced a better sequence identifier, one that combines an accession (which identifies a particular sequence record) with a version number (which tracks changes to the sequence itself). It is expected that this kind of Seq-id will become the preferred method of citing sequences. 

Users will still be able to retrieve a record based on the accession number alone, without having to specify a particular version. In that case, the latest version of the record will be obtained by default, which is the current behavior for queries using Entrez and other retrieval programs. 

The International Sequence Database Collaborators also started assigning accession, version numbers to protein sequences within the records. Previously, it was difficult to reliably cite the translated product of a given coding region feature, except 

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