Lab 2 and 3 Notes.docx

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Cell and Systems Biology
Ron Ammar

Lab 2 and 3 Summary Notes PSI-BLAST • Position-Specific Iterated BLAST • Highly sensitive that is extremely useful for finding distantly related proteins or new members of protein family • Use PSI-BLAST when standard protein-protein BLAST search either failed to find significant hits, or returned hits with descriptions such as “hypothetical protein” • PSI starts with a standard protein-protein BLAST and then uses these results to build up a more refined search that is tailored to your query over successive iterations of the search o Does this by building a position-specific scoring matrix (PSSM) – identifies the specific amino acid changes that are most likely to be present between your query sequence and similar database sequences o Position-specific scoring matrices are essentially substitution matrices tailored to your query of interest • Substitution matrices describe the likelihood that a residue will change over evolutionary time o They are scoring systems for comparing nucleotide or protein sequences that take into account constraints on the evolution of the sequences o Positive numbers indicate a high probability for going from one amino acid to another • Problems with PSI-BLAST: o Must assume that the database sequences are independent and that the sample space is large enough to represent the true underlying diversity of the family o
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