[Bioperl-l] Re: [Bioperl-guts-l] BioPerl::RefSeq usage

[Jason Stajich]

RefSeq only has, well, refseqs which are NC_, NM_, NP_, NT_, etc
accessions so hopefully you are only asking for refseq accessions.  Also,
the Bio::DB::RefSeq implementation talks to a server at the EBI which is
replicating the refseq db so it is possible it doesn't contain exactly
what is in Entrez unless the refseq db had been released and updated at
the EBI site.

-jason



On Thu, 13 Feb 2003, sroy at cs.unm.edu wrote:

> Hi,
> I am sorry if I have posted this earlier but I dont remember seeing it in
> the list.
> I am using BioPerl::RefSeq class to fetch me a sequence for a given
> accession number. I have noticed that for some accession numbers I do not
> get any entry. But the same query on Entrez:Protein gives me a hit.
> I am using BioPerl::get_Seq_by_acc API to get me the sequence.
> I wanted to know whether I am using the correct API to fetch the sequence
> or this there an API that fetches sequence from Entrez.
>
> Thank you,
> Sushmita
>
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--
Jason Stajich
Duke University
jason at cgt.mc.duke.edu