stop '*' symbol in Bio::AlignIO::fasta.pm

classic Classic list List threaded Threaded
2 messages Options
Reply | Threaded
Open this post in threaded view
|

stop '*' symbol in Bio::AlignIO::fasta.pm

Albert Vilella
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.

_______________________________________________
Bioperl-l mailing list
[hidden email]
http://portal.open-bio.org/mailman/listinfo/bioperl-l
Reply | Threaded
Open this post in threaded view
|

Re: 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.
>
> _______________________________________________
> Bioperl-l mailing list
> [hidden email]
> http://portal.open-bio.org/mailman/listinfo/bioperl-l

--
Jason Stajich
Duke University
http://www.duke.edu/~jes12


_______________________________________________
Bioperl-l mailing list
[hidden email]
http://portal.open-bio.org/mailman/listinfo/bioperl-l