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

[Georg Fuellen]

Hi,

I'm very happy that you're volunteering as the new caretaker
of the bioperl alignment resources..
the script you're looking for is at
http://www.techfak.uni-bielefeld.de/bcd/Perl/Bio/UnivAln-1.009/t/univaln.t2
Feel free to contact me further questions.

best wishes,
  georg
fuellen@alum.mit.edu
Ruhr-Universitaet Bochum, Spezielle Zoologie
http://www.techfak.uni-bielefeld.de/~fuellen/

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
> 
> 
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