[Bioperl-l] Protein ID to Gene ID

Hilmar Lapp hlapp at gmx.net
Sun Dec 18 23:22:20 EST 2005

GenBank has the protein-mRNA cross-reference in the feature table, 
hence you would need to look into the tag/value pairs of a sequence's 
features. DBSOURCE I believe is only present for those entries 
originating from UniProt (i.e., not natively from GenBank).

On top of all that, the tags GenBank uses for their entry annotation 
are not the ones BioPerl uses to tag its annotation objects - BioPerl 
is not an API solely for GenBank. Consult the Bio::SeqIO::genbank POD 
for documentation on what goes where in the BioPerl object model.


On Dec 16, 2005, at 6:13 AM, Miroslava Cuperlovic-Culf wrote:

> Dear All,
> I am trying to make a small program that would get the GeneBank gene 
> ID from
> GenBank protein ID. I think that DBSOURCE in GenBank entry for protein 
> has
> the number I need. So I wrote something like this:
> my $ac = $seq->annotation;
> my @values = $ac->get_Annotations('dblink');
> for my $value ( @values ) {
> print "DBSOURCE ", ",$value->tagname,$value->as_text,"\n";
> }
> But I get nothing. What is going on here? Any info/ideas would be 
> greatly
> appreciated,
> Sincerely,
> Mira
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Hilmar Lapp                            email: lapp at gnf.org
GNF, San Diego, Ca. 92121              phone: +1-858-812-1757

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