Class 4: Fast Sequence Alignment. Alignment in Real Life. One of the major uses of alignments is to find sequences in a “database” Such collections contain massive number of sequences (order of 10 6 )
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Problem (for local alignment):
Find (fast!) “good” diagonals and extend them to complete matches
tSignature of a Match
Assumption: good matches contain several “patches” of perfect matches
many close pairs.
…FSGTWYA… (query word is in green)
GTW 6,5,11 22
neighborhood ASW 6,1,11 18
word hits ATW 0,5,11 16
> threshold NTW 0,5,11 16
GTY 6,5,2 13
neighborhood GAW 9
tExtending Potential Matches