[Bioperl-l] Getting chromosome from GenPept?
Leo, Paul (NIH/NHGRI)
pleo at mail.nih.gov
Tue Jul 27 13:58:25 EDT 2004
I have a bunch of proteins denoted by their gi number from a Mass Spect.
Expt. which I want to organize. I get the protein "details" from
Bio::DB::GenPept using the GI number (want to find Gene names and other
properties etc ... ).
I also want the chromosome if it is available. I usually get these from
"primary_tag='source' tag='chromosome' in the sequence object but this is
not always present eg
Gi= 23272966 has no chromosome info (see
But if I following the link through the LocusID (CDS primary tag) to
LocusLink ( http://www.ncbi.nlm.nih.gov/LocusLink/LocRpt.cgi?l=11947
I find that it is chromosome 10....
What is the "Bio-Perl" way to get this info??? Otherwise I was just going to
get the $LocusID from the $seq object and get the page
<http://www.ncbi.nlm.nih.gov/LocusLink/LocRpt.cgi?l=$LocusID> ... strip the
HTML and then get the chromosome.
Is there a more sexy way to do this?
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