in reply to Is it possible to retrieve the coding sequence of a gene from NCBI GenBank database using perl ?
I know next to nothing about bioinformatics but perhaps this suggestion helps.
poj#!/usr/bin/perl use warnings; use strict; use Bio::DB::GenBank; use Bio::SeqIO; my $gb = new Bio::DB::GenBank; my $acc = "NM_021817"; my $seq1 = $gb->get_Seq_by_acc($acc); my $sequence = $seq1->seq; for my $feat ($seq1->get_SeqFeatures){ if ($feat->primary_tag eq 'CDS'){ print $feat->get_tag_values('product'),"\n"; print $feat->get_tag_values('gene'),"\n"; my $start = $feat->start; my $len = $feat->length; my $cds = substr($sequence,$start-1,$len); use Text::Wrap; # put this at top $Text::Wrap::columns = 71; print wrap('', '', $cds); } }
|
|---|
| Replies are listed 'Best First'. | |
|---|---|
|
Re^2: Is it possible to retrieve the coding sequence of a gene from NCBI GenBank database using perl ?
by supriyoch_2008 (Monk) on Jan 24, 2017 at 14:23 UTC |