[Bioperl-l] Reading GenBank Genomic File Annotation

[CHANDAN SINGH]

On 5/19/06, Staffa, Nick (NIH/NIEHS) [C] <staffa at niehs.nih.gov> wrote:
>
> Specifically:
> I have the document to which you refer,
> but have not seen this one thing I need in the printout of tags etc.:
> the values in this line;
>      mRNA            join(380..509,578..1913,7784..8649,9439..10200)
> Is that a  location object?


Yes it is a  location object .  If you  want  that  as a  string (this is
what seems  from ur mail ) , u just have to do this :

$loc = $fet->location();

$loc_str = $loc->to_FTstring() ;

Hope it helps.
Chandan

Nick Staffa
> Telephone: 919-316-4569  (NIEHS: 6-4569)
> Scientific Computing Support Group
> NIEHS Information Technology Support Services Contract
> (Science Task Monitor: Jack L. Field( field1 at niehs.nih.gov )
> National Institute of Environmental Health Sciences
> National Institutes of Health
> Research Triangle Park, North Carolina
>
>
> > ----------
> > From:         Brian Osborne
> > Sent:         Thursday, May 18, 2006 5:54 PM
> > To:   Staffa, Nick (NIH/NIEHS) [C]; bioperl-l at lists.open-bio.org
> > Subject:      Re: [Bioperl-l] Reading GenBank Genomic File Annotation
> >
> > Nick,
> >
> > Have you read the Feature-Annotation HOWTO? This would be a good
> starting
> > point...
> >
> > Brian O.
> >
> >
> > On 5/18/06 4:49 PM, "Staffa, Nick (NIH/NIEHS) [C]" <staffa at niehs.nih.gov
> >
> > wrote:
> >
> > > Would like a fairly simple way to extract certain information from
> Genbank
> > > Genomic File Annotations.
> > > Namely the six D.melanogaster sequences.
> > > Specifically to find gene entries and learn the gene name, begin and
> end and
> > > CDS.
> > > Please point me to appropriate modules and documentation.
> > >
> > >
> > > Nick Staffa
> > > Telephone: 919-316-4569  (NIEHS: 6-4569)
> > > Scientific Computing Support Group
> > > NIEHS Information Technology Support Services Contract
> > > (Science Task Monitor: Jack L. Field( field1 at niehs.nih.gov )
> > > National Institute of Environmental Health Sciences
> > > National Institutes of Health
> > > Research Triangle Park, North Carolina
> > >
> > >
> > > _______________________________________________
> > > Bioperl-l mailing list
> > > Bioperl-l at lists.open-bio.org
> > > http://lists.open-bio.org/mailman/listinfo/bioperl-l
> >
> >
> >
>
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