Bioinformatics: What Is PSI-BLAST?

Bioinformatics: What Is PSI-BLAST?

PSI-BLAST (Position-Specific Iterative BLAST) is a software designed for proteins, and it's a BLAST search that uses a PSSM (position-specific scoring matrix).

What is PSSM?

PSSM (position-specific scoring matrix) is a matrix used for biological data, and its main role in PSI-BLAST search is to increase the sensitivity of results.

PSI-BLAST search uses PSSM as a query instead of individual sequence, it's like a matrix constructed from a multiple sequence alignment and then each position of the alignment will have its own position specific score.

How PSI-BLAST works?

It begins with a normal BLAST search (the more match, the more score), but in this case a regular BLAST search will probably miss more distant and may be interesting homologies, so next PSI-BLAST will construct a PSSM (position-specific scoring matrix) and repeat the search until no new matches are found, this will result in finding new distant sequences that you are may be interested in.

You can read this post (Different Blast Programs) to understand all types of BLAST programs including PSI-BLAST and what each one do.

You can access PSI-BLAST from EBI website HERE.