<html><div style='background-color:'><DIV class=RTE>
<P>Thanks for your suggestions, but it's quite strange that there isn't any method to obtain a simple list of all refSeq Id's of a genome. </P>
<P>But, it is possible to obtain a complete list of all genes with another nomenclature (Locus ID, Accession number, etc...)?</P>
<P>Thanks. <BR></P></DIV>
<DIV></DIV>>From: "Sean Davis" <sdavis2@mail.nih.gov>
<DIV></DIV>>To: "Jeremy Semeiks" <jrs@farviolet.com>, "Tomas Marques" <tomas_marques@hotmail.com>, <bioperl-l@portal.open-bio.org>
<DIV></DIV>>Subject: Re: [Bioperl-l] Refseq Ids
<DIV></DIV>>Date: Sun, 19 Sep 2004 19:38:28 -0400
<DIV></DIV>>
<DIV></DIV>>I haven't checked rat directly, but I think they are also available at the
<DIV></DIV>>same place as genbank flat files, in case you need that detail.
<DIV></DIV>>
<DIV></DIV>>
<DIV></DIV>>----- Original Message -----
<DIV></DIV>>From: "Jeremy Semeiks" <jrs@farviolet.com>
<DIV></DIV>>To: "Tomas Marques" <tomas_marques@hotmail.com>;
<DIV></DIV>><bioperl-l@portal.open-bio.org>
<DIV></DIV>>Sent: Sunday, September 19, 2004 5:07 PM
<DIV></DIV>>Subject: Re: [Bioperl-l] Refseq Ids
<DIV></DIV>>
<DIV></DIV>>
<DIV></DIV>> > On Sat, Sep 18, 2004 at 09:59:46AM +0200, Tomas Marques wrote:
<DIV></DIV>> > > How can I obtain all RefSeq IDs from Rat genome? (using BioPerl, of
<DIV></DIV>> > > course...)
<DIV></DIV>> > >
<DIV></DIV>> > >
<DIV></DIV>> > >
<DIV></DIV>> > > I'm using Bio::DB::RefSeq but I have not been able to locate any
<DIV></DIV>> > > method(inherit or not)to do it...
<DIV></DIV>> >
<DIV></DIV>> > Hi Tomas,
<DIV></DIV>> >
<DIV></DIV>> > The most straightforward way to do this might be to download the rat
<DIV></DIV>> > Refseq files directly. They're at
<DIV></DIV>> >
<DIV></DIV>> > ftp://ftp.ncbi.nlm.nih.gov/refseq/R_norvegicus/
<DIV></DIV>> >
<DIV></DIV>> > You should be able to use the Bioperl FASTA parser (part of the SeqIO
<DIV></DIV>> > module) to parse these.
<DIV></DIV>> >
<DIV></DIV>> > HTH,
<DIV></DIV>> > Jeremy
<DIV></DIV>> > _______________________________________________
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<DIV></DIV>> > Bioperl-l@portal.open-bio.org
<DIV></DIV>> > http://portal.open-bio.org/mailman/listinfo/bioperl-l
<DIV></DIV>> >
<DIV></DIV>>
<DIV></DIV>>
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