On 13/11/08 1:00 PM, "Arnaud Kerhornou" <[EMAIL PROTECTED]> wrote:
> 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 ?
Hi Arnaud,
Yes it is. Let us investigate what's going on there and we'll get back to
you with a suggestion
A.
> Is there a way of fixing this translation issue ?
>
> Thanks
> Arnaud
