[Bioperl-l] AlignIO formats

[Peter Cock]

On Tue, Mar 30, 2010 at 9:10 PM, Bernd Web <bernd.web at gmail.com> wrote:
> Hi,
>
> Using GuessSeqFormat and AlignIO, I stumbled on some issues and
> am now wondering if the defined formats are actually OK. Esp. related to
> pfam, selex, stockholm formats it seems:
>
> pfam here is like selex without any comment lines, but with the
> /start-end after the seq id like myseq/1-111.
> The EBI site (http://www.ebi.ac.uk/2can/tutorials/formats.html#pfam)
> actually defines Pfam and Stockholm to be the same formats. This makes
> me wonder: is the Pfam format actually defined as Selex or Stockholm?
> Within BioPerl it is like Selex.

I (and therefore the Biopython documentation) also think PFAM
and Stockholm alignments are basically the same thing. The
BioPerl wiki seems to agree with this interpretation too.

Looking at the HMMER2 examples, Selex is different but the
comment style is similar. The obvious thing to check is the
presence or absence of the "# STOCKHOLM 1.0" header if
trying to tell them apart.

See also:
http://en.wikipedia.org/wiki/Stockholm_format and
http://www.bioperl.org/wiki/Stockholm_multiple_alignment_format
http://www.bioperl.org/wiki/SELEX_multiple_alignment_format

Peter