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lecture_2 - Pairwise Alignment(or models and algorithms are...

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Pairwise Alignment (or models and algorithms are your friend) Lecture 2 6.874J/7.90J/6.807 David Gifford
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Gene similarities revealed by dot plot promoter conservation Image removed for copyright reasons.
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Dot Plots Align subsequences of S1 and S2 ; place dot when score is high Image removed for copyright reasons.
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Pairwise Alignment (Global) Given a query sequence x , what is the best alignment to a sequence y ? (A, C, G, U, -) RNA (A, C, G, T, N, -, W, S, R, Y, K, M, B, D, H, V) DNA (20 letters, X, -) Protein s q probability of symbol s occurring at random in a sequence.
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Two possible models • Model R - Random– The sequences are unrelated and were generated by coin flips (biased) • Model M – Match – The sequences were derived from a common ancestor sequence
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A Probabilistic Model of Alignment = j y i x j i q q R y x P ) | , ( Joint probability that a and b have been originally derived from some (unknown) ancestor c (might be the same as a or b ) ab P = i y x i i P M y x P ) | , (
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The Odds Ratio Statistic (No Gaps) b a ab i i i i y x y x i y x y x q q P b a S y x S S q q P R y x P M y x P S q q P R y x P M y x P i i i i i i i i log ) , ( ) , ( log ) | , ( ) | , ( log ) | , ( ) | , ( = = = = =
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Example () 3 2 1 log
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This note was uploaded on 11/11/2011 for the course BIO 7.344 taught by Professor Bobsauer during the Spring '08 term at MIT.

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lecture_2 - Pairwise Alignment(or models and algorithms are...

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