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

Peter Schattner schattner@alum.mit.edu
Sun, 08 Oct 2000 13:38:59 -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