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

Peter Schattner schattner@alum.swarthmore.edu
Mon, 11 Sep 2000 10:02:02 -0700

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.


Peter Schattner