Hi,
Yes, but I think this issue has been fixed and should be already
commited in the CVS HEAD of the Ensembl API.
But I understood that martview is not using the Ensembl API to translate
transcripts sequences.
Arnaud
Alexandre Gattiker wrote:
Hello,
Bio::EnsEMBL::Transcript::translate calls
$peptide->translate(undef,undef,undef,$codon_table) without providing
the extra argument to Bio::PrimarySeqI::translate ($fullCDS or
$complete5) that causes the method to honour alternative start codons
in the genetic code. So the fix (which would also correct protview)
would be to pass that argument when appropriate from
Bio::EnsEMBL::Transcript::translate.
Alexandre
Arnaud Kerhornou wrote:
Hi everyone,
We are setting up a Mart database for bacterial genomes. I was
looking at the peptide sequence attribute. So far it seems fine
except sometimes the first amino acid which should be a Methionine is
displayed as a different amino acid.
Roughly, the rule is, if the CDS is complete and if the first amino
acid is not a methionine, then replace it by a methionine:
e.g. see Bioperl code, Bio::PrimarySeqI->translate():
## Only if we are expecting to translate a complete coding region
if ($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 ?
Is there a way of fixing this translation issue ?
Thanks
Arnaud
