[BiO BB] Re: PSI-BLAST query filter (Kevin Berney)

[Hongyu Zhang]

It's true that PSI-BLAST perhaps was not designed to be used as a
general purpose multiple alignment program as ClustalW was, but
according to my observation lots of time its result is better than
ClustalW. The problem of ClustalW is that, for a group of remote, and
sometimes not so remote, homologous sequences, it often gives
funny alignments. The situation can be worsened if the group has lots
of sequences; meanwhile, PSI-BLAST alignment is much better in
handling those situations. Again, for those who are not familiar with
NCBI-BLAST, it provides the "-m 1" option to print out the multiple
squence alignment instead of the default pair-wise alignment.

I assume most standard multiple sequence alignment methods are just
multi-steps of pair-wise alignments in an optimized order, while
profile methods are smarter in looking for some common
patterns in an iterated fashion. I used a GUI version of
ClustalW-based program a long long time ago (I forgot the
program name), which also provides a profile option in its menu, but I
didn't remember how well it works. Actually, some benchmarks on this
topic would be nice.

--
Hongyu Zhang
Computational biologist
Ceres Inc.