Lec03-local

Lec03-local - Local Alignment CMSC 423 Global, Semi-global,...

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Local Alignment CMSC 423
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Global, Semi-global, Local Alignments Last time, we saw a dynamic programming algorithm for global alignment: both strings s and t must be completely matched: Semiglobal: Local: Gaps at starts and ends of some sequences come for free Best alignment between substrings of s and t. s t t s s t
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Free gaps at ends of sequences best alignment between x and a prefx of y 0 1 2 3 4 5 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(n, m) best ignoring spaces matched to end of y x y C A G T T G C A A max of blue = A A G G T A T G A A T C best ignoring spaces matched to end of x max of orange =
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Free gaps at the start of sequences 0 1 2 3 4 5 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 0 0 0 0 0 0 0 0 0 0 0 0 ignore spaces matched to start of x x y C A G T T G C A A set blue = 0 to A A G G T A T G A A T C ignore spaces matched to start of y set orange = 0 to
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Semiglobal Recap Can combine these: e.g. to allow free spaces matched to the start of x and both ends of y: set bottom row and left-most column to 0 and take the max of the rightmost column. Free spaces matched to What to do end of x take max of topmost row end of y take max of rightmost column start of x set bottommost row to 0 start of y set leftmost column to 0
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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.
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This note was uploaded on 01/13/2012 for the course CMSC 423 taught by Professor Staff during the Fall '07 term at Maryland.

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Lec03-local - Local Alignment CMSC 423 Global, Semi-global,...

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