423f11-lec3

# 423f11-lec3 - Local Alignment CMSC 423 Representing edits...

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Local Alignment CMSC 423

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Representing edits as alignments prin-ciple |||| |||XX prinncipal (1 gap, 2 mm) misspell ||| |||| mis-pell (1 gap) prin-cip-le |||| ||| | prinncipal- (3 gaps, 0 mm) prehistoric |||||||| ---historic (3 gaps) aa-bb-ccaabb |X || | | | ababbbc-a-b- (5 gaps, 1 mm) al-go-rithm- || XX ||X | alKhwariz-mi (4 gaps, 3 mm)
Maximization vs. Minimization Edit distance: Sequence Similarity: replace min with a max and negate the parameters. gap penalty gap beneft (probably negative) cost score

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Local Alignment s t Local alignment between s and t: Best alignment between a subsequence of s and a subsequence of t. Motivation: Many genes are composed of domains , which are subsequences that perform a particular function.
0 1 2 3 4 5 6 7 8 9 10 11 12 9 8 7 6 5 4 3 2 1 0 9g 8g 7g 6g 5g 4g 3g 2g 1g 0 1g 2g 3g 4g 5g 6g 7g 8g 9g 10g 11g 12g OPT(i, j) OPT(i, j-1) OPT(i-1, j) OPT(i-1, j-1) i j Recall: Global Alignment Matrix OPT ( i , j ) contains the score for the best alignment between: the first i characters of string x [prefix i of x ] the first j character of string y [prefix j of y ] x y

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Local Alignment New meaning of entry of matrix entry: A[i, j] = best score between: some sufFx of x [1. .. i ] some sufFx of y [1. .. j ] 0 1 2 3 4 5 6 7 8 9 10 11 9 8 7 6 5 4 3 2 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 x y C A G T T G C A A A A G G T A T G A A T C Best alignment between a sufFx of x[1. .5] and a sufFx of y[1. .5]
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423f11-lec3 - Local Alignment CMSC 423 Representing edits...

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