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

Albert Vilella avilella at gmail.com
Fri Dec 30 11:36:13 EST 2005

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?



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