[BiO BB] Re: BiO_Bulletin_Board Digest, Vol 5, Issue 13

Hongyu Zhang forward at hongyu.org
Tue Mar 15 23:05:19 EST 2005

> The -m flag is cosmetic. The alignments you see are still  pairwise
> alignments to the query sequence, not a multiple alignment. -m 1

Iddo, I agree to most of your points, however, since PSI-BLAST uses
the PSSM (Position Specific Score Matrix), I would argue that the
final alignment contains more than just a pair-wise alignment. PSSM
is built upon the multiple sequences aligned in the previous round of

> 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 ?

Hi Deharshi. C/C++, Java and Perl are most important languages in
bioinformatics. C/C++ is more popular on speed sensitive
applications, while Java and Perl are more popular on database and
web related applications. C# is also catching up recently. In
addition to computer languages, you should take some classes on
algorithm development and statistics, which will make you more than
just a bioinformatics programmer.

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