[Bioperl-l] Clustalw.pm wrapper module checked in

Peter Schattner schattner@alum.mit.edu
Sun, 08 Oct 2000 13:46:07 -0700

Hello all

I have committed an "alpha" version of my Clustalw.pm bioperl module to
the bioperl-live (main) repository. There is also a test driver script
Clustalw.t that performs
some simple functional checks as well as an example script clustalw.pl.

The example script demonstrates using the module to monitor the
sensitivity of clustalw's output to variations in clustalw input
parameters (eg gap penalties, ktuple word
length) as well as monitoring clustalw's sensitivity to the order in
which the sequences are aligned.  Finally the script demonstrates how
clustalw can do local alignment by
using regular expression matching to find a location in each of the
sequences to be aligned to serve as an "anchor" for the alignment
process (this is similar in spirit to what
is done in the recent "dbclustal" program).

I would be grateful if any of you who do sequence alignment would try
the module out and let me know your thoughts on its utility and how it
might be improved.  I think it's
reasonably well documented, but if you find otherwise or run into any
bugs or problems that would be very helpful information for me.
Thanks.  You will need to have a
copy of clustalw on your machine (as well as downloading the main trunk
from the Bioperl CVS repository, of course).


Peter  Schattner