1 / 10

Neutral Substitution Rates

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

yana
Download Presentation

Neutral Substitution Rates

An Image/Link below is provided (as is) to download presentation Download Policy: Content on the Website is provided to you AS IS for your information and personal use and may not be sold / licensed / shared on other websites without getting consent from its author. Content is provided to you AS IS for your information and personal use only. Download presentation by click this link. While downloading, if for some reason you are not able to download a presentation, the publisher may have deleted the file from their server. During download, if you can't get a presentation, the file might be deleted by the publisher.

E N D

Presentation Transcript

  1. Neutral Substitution Rates

  2. 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

  3. 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

  4. Finding Conserved Elements

  5. Finding Conserved Elements (3) GERP

  6. Phylo HMMs HMM Phylogenetic Tree Model Phylo HMM

  7. Finding Conserved Elements (3)

  8. How do the methods agree/disagree?

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

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

More Related