[Bioperl-l] stop '*' symbol in Bio::AlignIO::fasta.pm
jason.stajich at duke.edu
Sat Dec 31 12:22:36 EST 2005
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
> 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?
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> Bioperl-l at portal.open-bio.org
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