title: PSI-BLAST tutorial.
abstract: 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.
authors.affiliation: National Center for Biotechnology, Information, National Library of Medicine, National Institutes of Health, USA.
authors.forename: Medha
authors.initials: M
authors.lastname: Bhagwat
authors.forename: L
authors.initials: L
authors.lastname: Aravind
mesh_terms: D000595:Amino Acid Sequence; D004258:DNA Polymerase III / Q000737:chemistry; D030541:Databases, Genetic; D004926:Escherichia coli / Q000201:enzymology; D016247:Information Storage and Retrieval; D008958:Models, Molecular; D008969:Molecular Sequence Data; D016415:Sequence Alignment; D017386:Sequence Homology, Amino Acid
chemical_list: D004258:DNA Polymerase III