1. CS273a Lecture 14, Fall 08, Batzoglou CS273a Lecture 14, 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

2. CS273a Lecture 14, Fall 08, Batzoglou CS273a Lecture 14, 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 C A A G

3. CS273a Lecture 14, Fall 08, Batzoglou CS273a Lecture 14, Fall 2008 Finding Conserved Elements

4. CS273a Lecture 14, Fall 08, Batzoglou CS273a Lecture 14, Fall 2008 Finding Conserved Elements (3) GERP

5. CS273a Lecture 14, Fall 08, Batzoglou CS273a Lecture 14, Fall 2008 Phylo HMMs HMM Phylogenetic Tree Model Phylo HMM

6. CS273a Lecture 14, Fall 08, Batzoglou CS273a Lecture 14, Fall 2008 Finding Conserved Elements (3)

7. CS273a Lecture 14, Fall 08, Batzoglou CS273a Lecture 14, Fall 2008 How do the methods agree/disagree?

8. CS273a Lecture 14, Fall 08, Batzoglou CS273a Lecture 14, Fall 2008 Statistical Power to Detect Constraint L N C: cutoff # mutations D: neutral mutation rate  : constraint mutation rate relative to neutral

9. CS273a Lecture 14, Fall 08, Batzoglou CS273a Lecture 14, Fall 2008 Statistical Power to Detect Constraint L N C: cutoff # mutations D: neutral mutation rate  : constraint mutation rate relative to neutral