[BiO BB] GI numbers

Stefanie Lager stefanielager at fastmail.ca
Wed Mar 31 05:44:26 EST 2004

Try linking them through LocusLink, either using one of the mapping
tables found at: ftp://ftp.ncbi.nih.gov/refseq/LocusLink/ or (a bit more
complicaated) using a system like OpenBNS: http://openbns.sourceforge.net/


> Hi,
> I'm analyzing a set of sequences with regard to their classifications
> as homologs from both COG and Kegg databases of orthologs. Although
> both COG and Kegg provide tables relating gene names to GI (PID)
> numbers, I'm, up to this moment, unable to map GIs from one dataset to
> the other, in order to check classifications for genes in both
> catalogs.
> GIs from COG appear to be from RefSeq and those from Kegg seem to be
> from GenPept. How can I map GI numbers from Kegg to GI numbers from
> COG database? Is there any query I can make to download such info for
> 185904 proteins in COG and their equivalents on Kegg Orthologs
> database?
> Here is an example:
> Sequence 14600509 is the protein coded by gene APE0180 from Aeropyrum
> pernix complete genome, as described in COG's table myva=gb. The same
> sequence is identified by GI 5103570 in Kegg. In this case, I was able
> map COG's GI to Kegg's GI by using the gene identifier and annotation,
> a procedure that is not easily automated.
> How can I retrive equivalent IDs for the whole COG gene set?
> Thanks in advance for any help.
> Robson
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