[Bioperl-l] codon tables, finding ORFs

[Chris Fields]

On May 21, 2010, at 3:48 PM, Robert Buels wrote:

> Chris Fields wrote:
> > 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
> 
> Oh they're available, CodonTable has a number of tables in it that you make translate() use optionally, and there are bacterial tables in there (but they are not well documented).  The default behavior is the 'NCBI standard' (eukaryotic) table that I linked to in the original post on this thread.
> 
> What I am looking for is a discussion of what the best default behavior of $seq->translate( -orf => 1 ) with no arguments should be.

Probably the simplest, with documentation on how to change it when needed.

> But also, there should be better documentation about the codon tables that are available, I can add that in my topic/longest_orf branch.
> 
> Rob

Agreed.  More docs never hurt.

chris