alignment-statistics

alignment-statistics - Alignment Statistics and...

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Alignment Statistics and Substitution Matrices BMI/CS 576 www.biostat.wisc.edu/bmi576/ Mark Craven craven@biostat.wisc.edu Fall 2011 Probabilistic model of alignments we’ll focus on protein alignments without gaps given an alignment, we can consider two possibilities R : the sequences are related by evolution U : the sequences are unrelated How can we distinguish these possibilities? How is this view related to amino-acid substitution matrices?
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Model for unrelated sequences we’ll assume that each position in the alignment is sampled randomly from some distribution of amino acids let be the probability of amino acid a the probability of an n -character alignment of x and y is given by 1 1 Pr( , | ) i i n n x y i i x y U q q = = = ! ! a q Model for related sequences we’ll assume that each pair of aligned amino acids evolved from a common ancestor let be the probability that evolution gave rise to amino acid a in one sequence and b in another sequence the probability of an alignment of x and y is given by ab p 1 Pr( , | ) i i n x y i x y R p = = !
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Probabilistic model of alignments How can we decide which possibility ( U or R ) is more likely? one principled way is to consider the relative likelihood of the
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alignment-statistics - Alignment Statistics and...

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