[Bioperl-l] from protein to nucleotide

[Jason Stajich]

I did post a way to do this a couple of weeks back - perhaps it will get
added to the FAQ at some point.

We definitely need FAQ volunteers, not
fair to put it all on Brian O.  If you see a good answer to question
adding it to the FAQ will help everyone out!

-jason
On Fri, 13 Jun 2003, Marc Logghe wrote:

> Hi Jack,
> You could do something like this:
>
>   foreach my $feat ( $seq->top_SeqFeatures() )
>   {
>     if ( $feat->primary_tag eq 'CDS' )
>     {
>       my ($id) = $feat->each_tag_value('coded_by'); # looks like
> 'coded_by="U05729.1:<1..122"'
>       # extract U05729.1 from it and get the sequence object from ncbi
>     }
>   }
>
> Of course you have to be sure that the CDS feature exists, including the
> coded_by tag.
> HTH,
> Marc
>
> > -----Original Message-----
> > From: Jack Chen [mailto:chenn at cshl.edu]
> > Sent: Friday, June 13, 2003 3:53 PM
> > To: bioperl-l at portal.open-bio.org
> > Subject: [Bioperl-l] from protein to nucleotide
> >
> >
> > Hi,
> >
> > Here is another question about GenBank sequence object. I am wondering
> > whether there is a convenient way to retrieve the nucleotide
> > sequence of a
> > protein with known gi number. For example, for protein
> > gi|497063|gb|AAB60473.1|, how should I get its corresponding
> > nucleotide?
> > Manually, I can get it by visiting the NCBI page and follow
> > the links. But
> > is there a way to do this automatically?
> >
> > Also, does anyone know how to parse the GenPept sequence
> > object to get the
> > 'DBSOURCE' field? For example, how can I get the accession number
> > 'U05729.1' from the following record? Thanks!
> >
> >
> > LOCUS       AAB60473                  39 aa            linear   ROD
> > 04-FEB-1995
> > DEFINITION  preproinsulin I.
> > ACCESSION   AAB60473
> > VERSION     AAB60473.1  GI:497063
> > DBSOURCE    locus MSU05729 accession U05729.1
> > KEYWORDS    .
> > SOURCE      Mus spretus (western wild mouse)
> >   ORGANISM  Mus spretus
> >             Eukaryota; Metazoa; Chordata; Craniata; Vertebrata;
> > Euteleostomi;
> >             Mammalia; Eutheria; Rodentia; Sciurognathi;
> > Muridae; Murinae;
> > Mus.
> >
> > Thanks,
> >
> > +-----O----------------------------------------+
> > |    o-o     Jack Chen, Stein Laboratory       |
> > |    o---o   Cold Spring Harbor Laboratory     |
> > |  o----o    1 Bungtown Road                   |
> > | O----O     Cold Spring Harbor, NY, 11724     |
> > | 0--o       Tel: 1 516 367 8394               |
> > |   O        Website: http://www.wormbase.org  |
> > |  o-o       e-mail: chenn at cshl.org            |
> > +-o---o----------------------------------------+
> >
> >
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> >
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--
Jason Stajich
Duke University
jason at cgt.mc.duke.edu