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paper_presentation - 7/29/10 BLO SU M 62 BLO cks of Amino...

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Unformatted text preview: 7/29/10 BLO SU M 62 BLO cks of Amino Acid SU bstitution M atrix By Steve & Jorja Henikoff 33 7/29/10 The old days  NO authentic scoring systems for sequence alignments.  First sequence comparisons on earth:--1 / mismatch & -1 / insertion or deletion 44 7/29/10 Alignment Scores  Sum of individual Log-odds Score The logarithm of the ratio of the likelihoods of the 2 hypotheses:- Pab the likelihood of the hypothesis we want to test fafb the likelihood of a null hypothesis (the 2 hypotheses are unrelated) 55    ,= = = 1 l log l l & l l l l 7/29/10 Positive scores = CONSERVATIVE SUBSTITUTION  Pab > fafb : Expect a and b aligned together in homologous sequences rather than just by chance Negative scores = NON-CONSERVATIVE 66 7/29/10 Remarkable characteristics in BLOSUM62 77 Amino acids pairs Scores Tryptophan (W/W) pairs +11 Leucine (L/L) pairs +4 Lysine-Glutamate (K/E) pairs +1 Alanine-Leucine (A/L) pairs-1 7/29/10...
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This note was uploaded on 07/29/2010 for the course BIOC BIOC2808 taught by Professor Dr.jjwang during the Fall '09 term at HKU.

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paper_presentation - 7/29/10 BLO SU M 62 BLO cks of Amino...

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