[Bioperl-l] Translating alternate start codons

Amir Karger akarger at CGR.Harvard.edu
Tue Nov 21 10:21:18 EST 2006


I think this is more a Bio question than a Bioperl question.

I did this:

#########
#!/usr/local/bin/perl

use strict;
use warnings;

use Bio::Seq;
use Bio::Tools::CodonTable;

my $seqobj = Bio::PrimarySeq->new (
    -seq => 'ATATGATAA',
    -id  => 'GeneFragment-12',
    -accession_number => 'X78121',
    -alphabet => 'dna',
);

$myCodonTable2  = Bio::Tools::CodonTable -> new ( -id => 4 );
my $is = $myCodonTable->is_start_codon('ATA') ? "is" : "is not";
print "ATA $is a valid start codon\n";
print "Table 4: ", $seqobj->translate("-codontable_id" => 4)->seq,"\n";
print "Table 1: ", $seqobj->translate("-codontable_id" => 1)->seq,"\n";
###########

I got this:
ATA is a valid start codon
Table 4: IW*
Table 1: I**

But EMBL tells me that EMBLCDS:AAT64955 starts with an M:
http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-id+3b6PL1TmQt3+-e+[EMBLCDS:'A
AT64955']+-qnum+1+-enum+3

So, does Bioperl purposely not translate start codons to M, while EMBL
does? Am I supposed to just change the I to M explicitly in my code? I
didn't see an obvious option to translate() to do it.

Thanks,

- Amir Karger
Research Computing
Life Sciences Division
Harvard University
617-496-0626



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