[Bioperl-l] Bio::SeqIO, genbank -> fasta, protein only?

Brian Osborne bosborne11 at verizon.net
Sat Oct 14 14:40:21 EDT 2006


Jay,

What you expected was that setting the -alphabet to "protein" would make
Bioperl translate the input nucleotide sequence to output protein. In
Bioperl this is accomplished by using the translate() method, no surprise
there. If you take a look at the documentation on translate() in the online
Bioperl Tutorial you'll see that this is a fairly sophisticated method, you
can do all sorts of different things with it. So using -alphabet for this
purpose won't really work, there are too many different ways to translate.

Brian O.


On 10/14/06 11:25 AM, "Jay Hannah" <jay at jays.net> wrote:

> Would it be a Good Thing if it did what I was expecting?




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