1 / 9

Midterm Review

Midterm Review. Review of previous weeks. Pairwise sequence alignment Scoring matrices PAM, BLOSUM, Dynamic programming Needleman-Wunsch (Global) Semi-global (no end-gap penalties) Smith-Waterman (Local). Review of previous weeks. Statistical significance of alignments

tsample
Download Presentation

Midterm Review

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. Midterm Review

  2. Review of previous weeks • Pairwise sequence alignment • Scoring matrices • PAM, BLOSUM, • Dynamic programming • Needleman-Wunsch (Global) • Semi-global (no end-gap penalties) • Smith-Waterman (Local)

  3. Review of previous weeks • Statistical significance of alignments • p-value, E-value, z-score? • Computing significance using random samples. • Example: • Suppose we have a face matching algorithm and we assign scores based on match of gender, complexion, eye-color, hair-color, use of glasses, use of face jewellery, existence of mustache, beard.

  4. Statistical significance • We match 100K pairs of faces randomly and here’s the (hypothetical) score distribution:

  5. Statistical significance • What is the p-value of a match with score 7? score 1?

  6. Statistical significance • p-value(x>=7) = 0.125

  7. Statistical significance • p-value(x>=1) = 0.875

  8. Statistical significance • p-value(x>=4) = 0.5

  9. Suffix Trees and Suffix Arrays • Construction of suffix trees and suffix arrays • Pattern search in suffix trees/arrays • Other applications • E.g., • Finding the most occurring pattern of length 2 in a string (Solution: count the # of leaves below the nodes that have string depth>=2)

More Related