[Bioperl-l] stop '*' symbol in Bio::AlignIO::fasta.pm

[Jason Stajich]

Yes it definitely makes sense.  They should be supported.

On Dec 30, 2005, at 11:36 AM, Albert Vilella wrote:

> Hi all,
>
> I just want to ask the bioperl community if it makes sense to have the
> stop '*' symbol in Bio::AlignIO::fasta.pm module.
>
> It makes sense to me when working on alignments of gene predictions  
> that
> happen to have stop codons in the middle of the sequences, it may not
> for other cases.
>
> For what I see, I needed to change this in line 58:
>
> $MATCHPATTERN = '^A-Za-z\.\-\*';
> #$MATCHPATTERN = '^A-Za-z\.\-';
>
> Do you think this could be included in the module?
>
> Bests,
>
>     Albert.
>
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--
Jason Stajich
Duke University
http://www.duke.edu/~jes12