[Bioperl-l] codon tables, finding ORFs

[Brian Osborne]

Rob,

The user will use translate(), which can do something like this:

$prot_obj = $my_seq_object->translate(-orf => 1,
                                      -start => "atg" );

CodonTable does little more than hold the codon/aa data. All the useful work is done by translate(), and there are lots of options. Here is part of the documentation:

 Returns : A Bio::PrimarySeqI implementing object
 Args    : -terminator    - character for terminator        default is *
           -unknown       - character for unknown           default is X
           -frame         - frame                           default is 0
           -codontable_id - codon table id                  default is 1
           -complete      - complete CDS expected           default is 0
           -throw         - throw exception if not complete default is 0
           -orf           - find 1st ORF                    default is 0
           -start         - alternative initiation codon
           -codontable    - Bio::Tools::CodonTable object
		   -offset        - offset for fuzzy locations      default is 0

 Notes   : The -start argument only applies when -orf is set to 1. By default
           all initiation codons found in the given codon table are used
           but when "start" is set to some codon this codon will be used
           exclusively as the initiation codon. Note that the default codon
           table (NCBI "Standard") has 3 initiation codons!


Brian O.

On May 21, 2010, at 1:44 PM, Robert Buels wrote:

> Hi all,
> 
> Right now, Bio::Tools::CodonTable uses as its 'standard' table the NCBI one, described at http://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi#SG1.
> 
> This table recognizes three different start codons: the usual ATG, plus TTG and CTG (which I'd never heard of before looking there, seems they are rare).
> 
> The issue is, if you use this codon scheme to find open reading frames in nucleotide sequences, you get some ORFs that I think a lot of biologists would be surprised at, from these two (rare?) start codons.
> 
> Seems to me, this might be a problem.  I mean, a naive user (which just about everyone is!) would expect the default codon table to only recognize the canonical ATG as a start, right?  And would be rather displeased if BioPerl said (by default) that something starting with one of these rare codons was an open reading frame?
> 
> So I guess my question is, do we think BioPerl (Bio::Tools::CodonTable) should really recognize these rare start codons by default?
> 
> Rob
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l