[Bioperl-l] Need info re Prodom & Stockholm formats and univaln.t2

[Kevin Howe]

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Hi Peter,

I have attached examples of prodom and stockholm format. For a more formal
description of the prodom format, look at the SRS icarus files:

ftp://ftp.toulouse.inra.fr/pub/prodom/prodom2000.1/4SRS/

For a more formal description of Stockholm format, check out

http://kisac.cgr.ki.se/cgr/groups/sonnhammer/Stockholm.html

Best,

Kevin






On Mon, 11 Sep 2000, Peter Schattner wrote:

> In developing the new "AlignIO.pm" module, I have been using various
> multiple-alignment data files ("test.pfam, "test.mase" etc) in the "/t"
> directory to confirm that the new module is parsing properly.
> 
> However, for the formats "prodom" and "stockholm" (which are included among
> the formats accepted by SimpleAlign.pm) I do not find any sample files. Can
> anyone out there send me  sample prodom- and/or stockholm-format multiple
> sequence alignment files so that I can test that the  new input modules for
> these formats are parsing correctly?
> 
> Also, in the module UnivAln.pm, there is reference to a script "univaln.t2"
> which more fully exercises the UnivAln module.  Does anyone out there (Ewan?,
> Georg?, Steve?) have a copy of this script they could send me?  I am trying
> to assess the feasibility and level of effort required to merge the
> functionalities of the SimpleAlign and UnivAln modules once multiple
> alignment IO has been stripped out using AlignIO.
> 
> Thanks.
> 
> Peter Schattner
> 
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l@bioperl.org
> http://bioperl.org/mailman/listinfo/bioperl-l
> 

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