[Bioperl-l] using Bio::DB::GenBank get translation

Vince Forgetta vince.forgetta at staff.mcgill.ca
Fri Dec 12 10:13:01 EST 2003


Hi all,

i have seen on some previous posts that you can retrieve the CDS start 
and stop from a GenBank DNA sequence accessionif the file is stored 
locally and read in using Bio::SeqIO. How would I retrieve the 
translation start and stop of a GenBank accession downloaded using 
Bio::DB::GenBank. For example, the code below does not seem to find a 
tag "translation":

use Bio::DB::GenBank;
my $gb = new Bio::DB::GenBank;
my $seq;
 my $accession;
 $seq = $gb->get_Seq_by_acc($accession);
 while (not(defined($seq)));
foreach my $feat ($seq->all_SeqFeatures()){
        my $CDS = "";
        if ($feat->has_tag('translation')){
        $CDS = $feat->start."..".$feat->end;
        return "$CDS\n";
    }else{
        return "Not found\n";
    }


Thank you for your time.



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