[Bioperl-l] How to get the corresponding DNA sequence of a protein gi#??

[Sally Li]

Jason,

Thank you for your codes. But the codes should be
modified as:
Before you run the script, you have to make directory
'tmp'.

# do some caching in the event you're pulling up the
same
# chromosome and/or you are debugging
my $cachent = new Bio::DB::FileCache(-kept =>1,
				     -file =>'./tmp/nt.idx',
				     -seqdb =>$ntdb);

my $cachepep = new Bio::DB::FileCache(-kept => 1,
				      -file =>'./tmp/pep.idx',
				      -seqdb =>$pepdb);



Sally


--- Jason Stajich <jason at cgt.mc.duke.edu> wrote:
> You might read my post here:
>
http://bioperl.org/pipermail/bioperl-l/2003-April/011918.html
> 
> This code works only when the protein record is
> annotated with back links
> coded_by
> 
> Of course this is more of an NCBI question if the
> back links are missing -
> we provide the tools not the data so if a link
> doesn't exist you have to
> get creative...
> 
> Things like -
> 
> Parse in the whole genome sequence and grab the
> annotated proteins from it
> and see which ones match the ones you are interested
> in.
> 
> a) get the genome sequence for the organism you have
> pep gi #
> b) tblastn
> c) cleanup alignment with genewise if these genes
> have introns.
> 
> -jason
> 
> On Mon, 21 Apr 2003, Sally Li wrote:
> 
> > Hi,
> >
> > The following is a blast result (partial) from
> > gi|29836496 (coronavirus genome's putative gene).
> >
> >
> > gi|547041
> >  gi|58980
> > gi|7769344
> >  gi|74849
> >
> > These are Genbank numbers. They are protein ids.
> We
> > can easiy obtain sequences based on these gi#
> using
> > bioperl modules. But how can I get the
> corresponding
> > DNA sequences?
> >
> > Thank you for your help.
> >
> > Sally
> >
> >
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> 
> --
> Jason Stajich
> Duke University
> jason at cgt.mc.duke.edu


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