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PSI-BLAST (Position-Specific Iterative Basic Local Alignment Search Tool) derives a position-specific scoring matrix (PSSM) or profile from the multiple sequence alignment of sequences detected above a given score threshold using protein-protein BLAST. This PSSM is used to further search the database for new matches, and is updated for subsequent iterations with these newly detected sequences. Thus, PSI-BLAST provides a means of detecting distant relationships between proteins. In this chapter, we discuss practical aspects of using PSI-BLAST and provide a tutorial on how to uncover distant relationships between proteins and use them to reach biologically meaningful conclusions.
Bhagwat et al. (Mon,) studied this question.