[Bioperl-l] codon tables, finding ORFs

[Chris Fields]

On May 21, 2010, at 3:11 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

Maybe it shouldn't be all by default, but I have personally worked with two (bacterial) genes that had alternative start codons (TTG, GTG), so they should be made available in some way.

chris