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