[Bioperl-l] Refseq Ids

[Barry Moore]

If you just want the IDs,  just grep 
ftp://ftp.ncbi.nih.gov/refseq/release/release-catalog/RefSeq-release7.catalog 
for the rat taxon id.

Barry

Marques Bonet wrote:

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