pairwise-alignment-2

pairwise-alignment-2 - Pairwise Sequence Alignment...

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Pairwise Sequence Alignment (Continued) BMI/CS 576 www.biostat.wisc.edu/bmi576/ Mark Craven craven@biostat.wisc.edu Fall 2011 Local alignment so far we have discussed global alignment , where we are looking for best match between sequences from one end to the other often we want a local alignment , the best match between subsequences of x and y
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Example local alignment aligning my name against the sequence for dTDP-4-dehydrorhamnose reductase from the bacterium opitutus terrae …LSGAYHLAASGHTSWHGFASAIIDLMPLD ARKCRAVE AIT… M ARKCRAVE N Local alignment motivation useful for comparing protein sequences that share a common motif (conserved pattern) or domain (independently folded unit) but differ elsewhere useful for comparing DNA sequences that share a similar motif but differ elsewhere useful for comparing protein sequences against genomic DNA sequences (long stretches of uncharacterized sequence) more sensitive when comparing highly diverged sequences
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Local alignment DP algorithm original formulation: Smith & Waterman, Journal of Molecular Biology , 1981 interpretation of array values is somewhat different: F ( i, j ) = score of the best alignment of a suffix of x [1… i ] and a suffix of y [1… j ] Local alignment DP algorithm F ( i , j ) = max F ( i " 1, j " 1) + s ( x i , y j ) F ( i " 1, j ) " d F ( i , j " 1) " d 0 # $ % % % % the recurrence relation is slightly different than for global algorithm
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This note was uploaded on 12/15/2011 for the course BMI 576 taught by Professor Staff during the Fall '11 term at Wisc Green Bay.

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pairwise-alignment-2 - Pairwise Sequence Alignment...

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