[Bioperl-l] Translating alternate start codons

Brian Osborne bosborne11 at verizon.net
Tue Nov 21 14:58:00 EST 2006


Amir,

I think I understand your question, perhaps not, and I think the recommended
solution is to create your own "custom" codon table. See t/CodonTable.t for
an example. 

Brian O.



On 11/21/06 11:16 AM, "Amir Karger" <akarger at CGR.Harvard.edu> wrote:

>> From: Brian Osborne [mailto:bosborne11 at verizon.net]
>> 
>> Amir,
>> 
>> The best documentation for translate() is in the online
>> Bioperl Tutorial,
>> have you checked that?
>> 
>> Brian O.
> 
> Thanks for the quick response. The tutorial is quite informative.
> It seems to me that the POD needs to document -complete more thoroughly,
> though:
> 
>                   Or if you expect a complete coding sequence (CDS)
> translation,
>                   with inititator at the beginning and terminator at the
> end:
> 
>                   $protein_seq_obj = $cds_seq_obj->translate(-complete
> => 1);
> 
> This doesn't really explain what it does.
> 
> I guess -complete was chosen as a compromise between having too many
> options and having lots of functionality. In my case, I want to keep the
> *, and I don't want warnings about terminators in the middle, because
> I've got a bunch of pseudogenes. So I'll just translate the M myself.
> 
> I'm sure you've had many "the documentation is spread out in too many
> places" discussions before, and I know keeping docs up to date is Hard.
> Oh well.
> 
> -Amir
> 
>> 
>> 
>> On 11/21/06 10:21 AM, "Amir Karger" <akarger at CGR.Harvard.edu> wrote:
>> 
>>> 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
>>> 
>>> _______________________________________________
>>> Bioperl-l mailing list
>>> Bioperl-l at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>> 
>> 
>> 
> 
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