[Bioperl-l] Re: How to get protein ID and get protein accession from GI

Siddhartha Basu sidd.basu at gmail.com
Wed Jun 4 10:54:13 EDT 2008


Hi,
You have to get the 'Feature' object for that.

On Tue, 03 Jun 2008, Ousmane Diallo wrote:

> hello,
> Could somebody help me on how to get the protein ID and ACCESSION using the mRNA gi or accession.
>
>
> my $db_obj = Bio::DB::GenBank->new();    my $seq_obj = 
> $db_obj->get_Seq_by_acc('123456') ;   # I pass here the mrna acc to get the 
> seq_obj
> my $gi = $seq_obj->primary_id ;                     # I get here the gi

my ($feat) = grep { $_->primary_tag() eq 'Protein' } $seq_obj->get_SeqFeatures();
print $feat->seq_id(),"\n";

For details and explanations read the Howto here .....

http://www.bioperl.org/wiki/HOWTO:Feature-Annotation

-siddhartha

>
>
> I need to get the protein ID and protein ACCESSION"
>
> THANKS!!
>
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