[Bioperl-l] Bio::AlignIO::metafasta tests

Chris Fields cjfields at uiuc.edu
Tue Jun 6 10:30:17 EDT 2006


Sendu,

This is Heikki's original submission for the specs for meta format:

http://article.gmane.org/gmane.comp.lang.perl.bio.general/1370/match=meta+fa
sta

So it's really a specialized FASTA format used to store meta information
about sequences.  Seems mainly useful for amino acid sequences, but is
extended to include properties of nucleotides like DNA content, RNA sec.
structure, and so on.  

Chris

> -----Original Message-----
> From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-
> bounces at lists.open-bio.org] On Behalf Of Sendu Bala
> Sent: Tuesday, June 06, 2006 4:18 AM
> To: bioperl-l at lists.open-bio.org
> Subject: Re: [Bioperl-l] Bio::AlignIO::metafasta tests
> 
> Chris Fields wrote:
> > Heikki,
> >
> > I uncovered a weird bug concerning Bio::AlignIO::metafasta which popped
> up
> > when running AlignIO.t (I was fixing bug 2000):
> >
> > http://bugzilla.open-bio.org/show_bug.cgi?id=2016
> >
> > Not sure what's going on there but using read_aln and write_aln seem to
> work
> > normally.  It may have something to do with Bio::SimpleAlign but I'm not
> > absolutely sure.
> >
> > Any ideas what may be going on here?
> 
> Yes, see my replies on the bug page. But so more people see the
> question, I'll ask here: can anyone offer examples of metafasta files,
> especially multiple alignments?
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