[mart-dev] Mart peptide translation question

[Arnaud Kerhornou]

Hi everyone,

We are setting up a Mart database for bacterial genomes. I was looking 
at the peptide sequence attribute. So far it seems fine except sometimes 
the first amino acid which should be a Methionine is displayed as a 
different amino acid.

Roughly, the rule is, if the CDS is complete and if the first amino acid 
is not a methionine, then replace it by a methionine:

e.g. see Bioperl code, Bio::PrimarySeqI->translate():

  ## Only if we are expecting to translate a complete coding region
   if ($complete) {
        # ...
        # if the initiator codon is not ATG, the amino acid needs to be 
changed to M
        if ( substr($output,0,1) ne 'M' ) {
            if ($codonTable->is_start_codon(substr($seq, 0, 3)) ) {
                $output = 'M'. substr($output,1);
            }    elsif ($throw) {
                $self->throw("Seq [$id]: Not using a valid initiator 
codon!");
            } else {
                $self->warn("Seq [$id]: Not using a valid initiator 
codon!");
            }
        }
   }

How do you translate CDS sequences in Martview, is it made on the fly 
within the Biomart perl API ?
Is there a way of fixing this translation issue ?

Thanks
Arnaud