neutral substitution rates
DESCRIPTION
Neutral Substitution Rates. 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. Finding Conserved Elements (2). A. C. Parsimony Method - PowerPoint PPT PresentationTRANSCRIPT
CS273a Lecture 10, Aut 08, BatzoglouCS273a Lecture 10, Fall 2008
Neutral Substitution Rates
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
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
CS273a Lecture 10, Aut 08, BatzoglouCS273a Lecture 10, Fall 2008
Finding Conserved Elements
CS273a Lecture 10, Aut 08, BatzoglouCS273a Lecture 10, Fall 2008
Finding Conserved Elements (3)
GERP
CS273a Lecture 10, Aut 08, BatzoglouCS273a Lecture 10, Fall 2008
Phylo HMMs
HMM
Phylogenetic Tree Model
Phylo HMM
CS273a Lecture 10, Aut 08, BatzoglouCS273a Lecture 10, Fall 2008
Finding Conserved Elements (3)
CS273a Lecture 10, Aut 08, BatzoglouCS273a Lecture 10, Fall 2008
How do the methods agree/disagree?
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
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