Re: Is it possible to retrieve the coding sequence of a gene from NCBI GenBank database using perl ?

[poj]

I know next to nothing about bioinformatics but perhaps this suggestion helps.

#!/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);
  }
}

poj

[supriyoch_2008]

Hi poj

Thank you for your valuable suggestions. The code works nicely and my problem is now solved.

With kind regards,

supriyoch_2008