ECS124_Lecture5

ECS124_Lecture5 - ECS 124: Theory and practice of...

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ecture 5: LCS, BLAST and DB Search ECS 124: Theory and practice of bioinformatics Lecture 5: LCS, BLAST and DB Search Instructor: IliasTagkopoulos itagkopoulos@ucdavis.edu Office: Kemper 3063 and GBSF 5313 4/20/2010 UC Davis 1
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Announcements c Make-up class c Midterm 4/20/2010 UC Davis 2 c Labs
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LAST TIME: Global vs. Local alignment Global alignment Local alignment 4/20/2010 3 Initialization: Iteration: Starting Position: Ending Position: F(0,j) = -j*d , F(i,0)=-i*d F(0,j) = F(i,0)= 0 F(i,j) = max{F(i-1,j) – d, F(i,j-1) – d, F(i-1,j-1) + Sim(S1 i ,S2 j )} Top left Bottom right F(i,j) = max{0, F(i-1,j) – d, F(i,j-1) – d, F(i-1,j-1) + Sim(S1 i ,S2 j )} anywhere anywhere
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Dot plots c c Alpha chain vs. beta chain of human hemoglobin (window 31, matches +5, mismatches -4) c (1)deletion, (2)insertion, (3) mutation 4/20/2010 UC Davis 4
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Some definitions c Definitions: Assume string with length n, then c Prefix of a string: the first k characters of the string, where k≤n c Suffix of a string: the last k characters of the string here n 4/20/2010 UC Davis 5 where k≤n c Substring : a prefix of a suffix, or equivalently a suffix of a prefix of the string c Subsequence : any combination of the characters in the string, without changing the order
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c Should gaps in the ends be penalized the same as any other gaps? agine Shotgun sequencing
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This note was uploaded on 05/30/2010 for the course ECS ECS 124 taught by Professor Tagkopoulos during the Spring '10 term at UC Davis.

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ECS124_Lecture5 - ECS 124: Theory and practice of...

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