[Bioperl-l] Refseq Ids

[Jason Stajich]

On Sep 20, 2004, at 5:21 AM, 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...)?

Try EnsMart: http://www.ensembl.org

>
> 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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>  > >
>  >
>  >
>
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--
Jason Stajich
jason.stajich at duke.edu
http://www.duke.edu/~jes12/