Hi Arnaud,
As I understand, you are replicating 'ensembl vertebrates' data model
for your 'bacterial genomes'. In Ensembl Vertebrates, the information
for changing the first amino acid to 'methionine' comes as a
post-translation modification, which sits in a separate database column.
Please see if thats the case in your mart too.
Thanks
Syed
Arek Kasprzyk wrote:
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
