[Bioperl-l] codon tables, finding ORFs

[Robert Buels]

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.

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