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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Class 4: Fast Sequence Alignment
Problem (for local alignment):
Find (fast!) “good” diagonals and extend them to complete matches
Assumption: good matches contain several “patches” of perfect matches
many close pairs.
…FSGTWYA… (query word is in green)
BLAST: phase 1
GTW 6,5,11 22
neighborhoodASW 6,1,11 18
word hitsATW 0,5,1116
> threshold NTW 0,5,1116