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

Brian Osborne bosborne11 at verizon.net
Fri Oct 13 21:20:40 UTC 2006


Yes, people use the -alphabet parameter. If you set it to something then
Bioperl will not try to determine whether the sequence is protein, rna, or
dna and this is particularly useful when the sequence contains characters
that Bioperl would object to (sequences with distasteful characters can be
created by various applications, for example, or you might introduce some
weird character for some reason). Setting the -alphabet would also speed up
Bioperl a bit, for the same reason.

Brian O.

On 10/13/06 2:56 PM, "Jay Hannah" <jay at jays.net> wrote:

> I just thought that -alphabet and molecule() would do that stuff for me? What
> else would "protein" mean in those? 

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