Genbank Replaced Sequences Lookup

Question

[Steve Metropolis]

Every now and then sequences disappear from genbank and are replaced by new ones, e.g. the BLAST - NCBI website show this record:

GenBank: AL591898.1
! This sequence has been replaced by FO393423.

Is there a table available for download that maps locus or gi numbers of replaced sequences to locus or gi numbers of the new sequence?

I would need this for around 80000 records.

Answer 1

[Woa]

I've followed this way to check the status of the RefSeq entires:

Knowing the status for Obsolete RefSeq entries

Answer 2

[Hamish]

When you are looking for a specific sequence version (e.g. AL591898.1 or GI:14330235) NCBI Entrez will attempt to return that specific version of the sequence, thus you sometimes get a message saying that the entry has been superseded by a new entry. Due to the way tracking of accessions works in GenBank (and various other databases) you can get the current version of the entry directly by querying the accession field with the unversioned accession:

AL591898[Accession]

Obviously this does not work for NCBI gi numbers, since they are specific to the sequence version and not related between versions. NCBI Entrez does have access to this information and uses it to construct the "Revision History" report for an entry, but I can not see a way to get at this via E-utilities.

For INSDC (DDBJ, EMBL-Bank and GenBank) accessions you cold use the ENA Sequence Version Archive to look-up the current version and get a revision history, but that won't help you with NCBI gis or RefSeqs.