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

debarshi roy vetdebarshi at gmail.com
Fri Mar 11 15:22:47 EST 2005

Hi Mr.Zhang,

I am a Graduate student in Biology major in Wichita State University.
I am interested to join in the Bioinformatics Lab in my University and
start my research works on  gene expression and some other on going
projects of K-BRIN program.
Could you please help me by providing with some basic informations?
I would like to know aboput the prerequisite knowledge for
Bioinformatics research What are computer programming language which
are of most importance?
and what are the lab techniques needed ?
Earlier I have done Bachelors of Veterinary sc and animal Husbandry from India.
Please give me the informations I will be very much greatful to you.

Dr.Debarshi Roy

On Fri, 11 Mar 2005 11:24:11 -0800, Hongyu Zhang <forward at hongyu.org> wrote:
> 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.
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