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

Georg Fuellen fuellen@alum.mit.edu
Tue, 12 Sep 2000 12:07:55 +0200 (MET DST)


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
Feel free to contact me further questions.

best wishes,
Ruhr-Universitaet Bochum, Spezielle Zoologie

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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