[ssml] Howto generate position specific score matrix (PSSM) in the way of psi-blast ?

[Jarod]

Hi,

I try to write a short program to generate position specific score matrix 
(PSSM) from a multi-alignment of sequences in Perl language, I know there are 
methods to do this, but I want to do this like PSI-blast. Unfortunately, the 
original article about PSI-blast does not make me clear, and the NCBI source 
code is too difficult to read. 

Anyone who can tell me the its principle and how psi-blast works?

Thanks.

         Jarod