[Bioperl-l] Sequence IDs

Heikki Lehvaslaiho heikki at ebi.ac.uk
Fri Mar 26 09:55:17 EST 2004


In my best knowledge there is not yet a global system for gene idenfiers, so I 
can not help you there.

GenBank, EMBL and DDBJ have agreed on using accession numbers (AC line) as 
unique, global identifiers. All other IDs are unique only within a single 


On Friday 26 Mar 2004 01:48, Robson Francisco de Souza wrote:
> Hi,
> This is not quite a bioperl question, but maybe there is some useful
> code in bioperl that can easy the task below.
> I'm trying to automatically track GI changes for a sequence in Genbank,
> so that I can list all GI numbers associated to a gene in a complete
> genome from Genbank, EMBL or Kegg. I need this to compare results from
> Kegg Orthologs database (GenomeNet), COG database (NCBI) and the String
> server from EMBL.
> Although I was able to download Kegg release 29, GI numbers for genes in
> this release are outdated and do not agree with COG GIs. Does anybody
> know of a way to retrive all GIs (PID) for every genes in complete genomes?
> Also, what is the unique ID or accession key for protein/dna
> sequence that is used by all main sequence databases (Genbank,
> SP/TrEMBL, DDBJ), if there is any? I couldn't find an easy way to cross
> results from analysis that employ identifications from different
> databases.
> Thanks for any help.
> Robson
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     _/  _/  _/  Heikki Lehvaslaiho    heikki_at_ebi ac uk
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