[Bioperl-l] need help urgently

[Smithies, Russell]

Grab the gene2accession list from here and do lookups.
Probably the fastest and easiest way.


Russell Smithies 

Bioinformatics Applications Developer 
T +64 3 489 9085 
E  russell.smithies at agresearch.co.nz 

Invermay  Research Centre 
Puddle Alley, 
Mosgiel, 
New Zealand 
T  +64 3 489 3809   
F  +64 3 489 9174  
www.agresearch.co.nz 





> -----Original Message-----
> From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-
> bounces at lists.open-bio.org] On Behalf Of Neeti Somaiya
> Sent: Saturday, 5 September 2009 12:21 a.m.
> To: Emanuele Osimo; bioperl-l
> Subject: Re: [Bioperl-l] need help urgently
> 
> Thanks. Its an interesting tool.
> 
> But I want to do this programatically.
> 
> I have gene ids to start with. Cant find a method to directly get
> sequence with gene id as input. So using the method of getting
> sequence with accession as input, for which I need to know accessions
> for my gene ids first. Is this a right approach? Please guide me. My
> main aim is to get the nucleotide sequence of a gene from ids entrez
> gene id/gene name. PLease guide me. I am confused.
> 
> -Neeti
> Even my blood says, B positive
> 
> 
> 
> On Fri, Sep 4, 2009 at 5:35 PM, Emanuele Osimo<e.osimo at gmail.com> wrote:
> > Try this:
> > http://david.abcc.ncifcrf.gov/conversion.jsp
> >
> > Emanuele
> >
> >
> > On Fri, Sep 4, 2009 at 12:13, Neeti Somaiya <neetisomaiya at gmail.com> wrote:
> >>
> >> Thanks for the replies.
> >>
> >> So the get seq by accession/GI worked for me. Now can anyone tell me
> >> the easiest way to get the GI /Accession of a gene from the gene
> >> id/gene name?
> >>
> >> -Neeti
> >> Even my blood says, B positive
> >>
> >>
> >>
> >> On Fri, Sep 4, 2009 at 2:47 PM, Neeti Somaiya<neetisomaiya at gmail.com>
> >> wrote:
> >> > Thanks for the link.
> >> > So I need only the following lines of code to get the sequence?
> >> >
> >> > use Bio::DB::GenBank;
> >> > $db_obj = Bio::DB::GenBank->new;
> >> > $seq_obj = $db_obj->get_Seq_by_id(2);
> >> >
> >> > How do I print the sequence?
> >> > $seq_obj->seq ??
> >> >
> >> > -Neeti
> >> > Even my blood says, B positive
> >> >
> >> >
> >> >
> >> > On Fri, Sep 4, 2009 at 1:31 PM, K. Shameer<shameer at ncbs.res.in> wrote:
> >> >>
> >> >> Retrieving a sequence from a database : BioPerl HOWTO
> >> >> http://bit.ly/RWIot
> >> >>
> >> >> Trust this helps,
> >> >> Khader Shameer
> >> >> NCBS - TIFR
> >> >>
> >> >>> Hi,
> >> >>>
> >> >>> I have an input list of gene names (can get gene ids from a local db
> >> >>> if required).
> >> >>> I need to fetch sequences of these genes. Can someone please guide me
> >> >>> as to how this can be done using perl/bioperl?
> >> >>>
> >> >>> Any help will be deeply appreciated.
> >> >>>
> >> >>> Thanks.
> >> >>>
> >> >>> -Neeti
> >> >>> Even my blood says, B positive
> >> >>> _______________________________________________
> >> >>> Bioperl-l mailing list
> >> >>> Bioperl-l at lists.open-bio.org
> >> >>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> >> >>>
> >> >>
> >> >>
> >> >>
> >> >
> >> _______________________________________________
> >> Bioperl-l mailing list
> >> Bioperl-l at lists.open-bio.org
> >> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> >
> >
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