Download - Neutral Substitution Rates
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CS273a Lecture 10, Aut 08, BatzoglouCS273a Lecture 10, Fall 2008
Neutral Substitution Rates
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CS273a Lecture 10, Aut 08, BatzoglouCS273a Lecture 10, Fall 2008
Finding Conserved Elements (1)
• Binomial method 25-bp window in the human genome Binomial distribution of k matches in N bases given the neutral
probability of substitution
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CS273a Lecture 10, Aut 08, BatzoglouCS273a Lecture 10, Fall 2008
Finding Conserved Elements (2)
• Parsimony Method Count minimum # of mutations explaining each column Assign a probability to this parsimony score given neutral model Multiply probabilities across 25-bp window of human genome
A
CAAG
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CS273a Lecture 10, Aut 08, BatzoglouCS273a Lecture 10, Fall 2008
Finding Conserved Elements
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CS273a Lecture 10, Aut 08, BatzoglouCS273a Lecture 10, Fall 2008
Finding Conserved Elements (3)
GERP
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CS273a Lecture 10, Aut 08, BatzoglouCS273a Lecture 10, Fall 2008
Phylo HMMs
HMM
Phylogenetic Tree Model
Phylo HMM
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CS273a Lecture 10, Aut 08, BatzoglouCS273a Lecture 10, Fall 2008
Finding Conserved Elements (3)
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CS273a Lecture 10, Aut 08, BatzoglouCS273a Lecture 10, Fall 2008
How do the methods agree/disagree?
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CS273a Lecture 10, Aut 08, BatzoglouCS273a Lecture 10, Fall 2008
Statistical Power to Detect Constraint
L
N
C: cutoff # mutationsD: neutral mutation rate: constraint mutation rate relative to neutral
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CS273a Lecture 10, Aut 08, BatzoglouCS273a Lecture 10, Fall 2008
Statistical Power to Detect Constraint
L
N
C: cutoff # mutationsD: neutral mutation rate: constraint mutation rate relative to neutral