[Bioperl-l] finding sequence 2000 bp upstream in bioperl?
Kevin.M.Brown at asu.edu
Wed Jul 2 15:36:43 EDT 2008
Get the start point for a Sequence Feature and request a subseq of the
main object that starts 2000 above that.
my $gb = new Bio::DB::GenBank;
$entry = $gb->get_Seq_by_id($id);
foreach my $f ($entry->all_SeqFeatures())
if ($f->primary_tag eq 'CDS')
my $seq = $entry->subseq($f->start - 2000,$f->start -
> -----Original Message-----
> From: bioperl-l-bounces at lists.open-bio.org
> [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of
> RICHARD GREEN
> Sent: Wednesday, July 02, 2008 11:10 AM
> To: bioperl-l at lists.open-bio.org
> Subject: [Bioperl-l] finding sequence 2000 bp upstream in bioperl?
> Howdy Bioperlers,
> Quick question, I have scripts that pull out a sequence from
> genbank, but I am looking for a command that would extract
> 2000 base pairs upstream of the sequence. Is there a way to
> extract just the Gene promoter region from genbank? Any
> advice that folks can give me a is muchly appreciated.
> Thanks again
> -Rich Green
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
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