lect 10 protein overview0

# lect 10 protein overview0 - Bioc 2808 Lecture 10 Overview...

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Click to edit Master subtitle style 7/29/10 Bioc 2808 Lecture 10 Overview of protein Instructor Dr. Junwen Wang

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7/29/10 Dealing with protein sequences Dynamic programming Pairwise sequence alignments Global alignment (Needlman-Wunch algorithm) Local alignment (Smith-Waterman algorithm) Scoring function Substitution matrices Gap penalties
7/29/10 Dynamic programming Initialization Matrix Fill or Scoring Traceback

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7/29/10 Most probable path: Viterbi algorithm - P(S) =0.6 P(A) =0.4 P(Y) =0.67 P(F)= 0.33 P(R) =0.13 P(Q) =0.07 P(A) =0.2 • • • 0. 4 0. 6 0. 6 0. 8 0. 2 0. 4 0. 0 0. 0 0. 0 0. 0 DYAF 0. 0 0. 0 1. 0 F in M4 max{0.00128*0.6*0.33, 0.00096*0*0.33, 0} F in I4 max{0, 0, 0} F in D4 P(v 4) P(N) =0.6 P(D) =0.4 P(F)= 0.8 P(Y) =0.2 1. 0 P(v1) P(v2) P(v3) P(v4) M1 I1 D1 M2 I2 D2 M3 I3 D3 M4 I4 D4 D 0.4 Y 0.008 A 0.0012 8 6 0 Trace back: M4->M3->M2->M1 Alignment: DYAF
7/29/10 55 Comparison with divide-and- conquer Divide-and-conquer algorithms split a problem into separate subproblems, solve the subproblems, and combine the results for a solution to the original problem Example: Quicksort Example: Mergesort Example: Binary search Divide-and-conquer algorithms can be thought of as top-down algorithms In contrast, a dynamic programming algorithm proceeds by solving small problems, then combining them to find the solution to larger

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## This note was uploaded on 07/29/2010 for the course BIOC BIOC2808 taught by Professor Dr.jjwang during the Fall '09 term at HKU.

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lect 10 protein overview0 - Bioc 2808 Lecture 10 Overview...

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