[Bioperl-l] codon tables, finding ORFs

[Brian Osborne]

Rob,

translate() is one of these methods where reading the documentation is required. Or to put it another way, if you tried to use it without reading the docs most of the time you'd get a result that differs from what you wanted, given the variety of ways to use it, quite apart from the issue of the 3 initiation codons.

So really, you have to read the docs, and they say:

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!

My concern right now is that CPAN has removed this text and more!

If you wanted to add an additional codon table and make it a default I have no problem with that. But, the "naive user" who doesn't read the documentation is probably still going to get "surprising" results. I don't think there's any way around RTFM for this method, changing the default table does not change this.

Brian O.

On May 21, 2010, at 4:11 PM, Robert Buels wrote:

> Brian Osborne wrote:
>> The user will use translate(), which can do something like this:
>> $prot_obj = $my_seq_object->translate(-orf => 1,
>>                                      -start => "atg" );
> 
> Yes, translate() has some non-default options for overriding this behavior. This doesn't address the question of whether including these other start codons is a good default.
> 
> Rob