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Finding Conserved Elements (1)

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 Count minimum # of mutations explaining each column

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Finding Conserved Elements (1)

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  1. 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. Finding Conserved Elements (2) A C • 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 A G

  3. Finding Conserved Elements

  4. Finding Conserved Elements (3) GERP

  5. Phylo HMMs HMM Phylogenetic Tree Model Phylo HMM

  6. Finding Conserved Elements (3)

  7. How do the methods agree/disagree?

  8. Statistical Power to Detect Constraint N L C: cutoff # mutations D: neutral mutation rate : constraint mutation rate relative to neutral

  9. Statistical Power to Detect Constraint N L C: cutoff # mutations D: neutral mutation rate : constraint mutation rate relative to neutral

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