Class 4: Sequence Alignment II Gaps, Heuristic Search. Alignment with Gaps – Example. 1. 2. Gaps. Both alignments have the same number of matches and spaces but alignment 2 seems better Definition : A gap is any maximal, consecutive run of spaces in a single string.
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Open gap: -2
Open gap: -2, each space: -1
Open gap: -2, gap length: -logn
We divide all possible alignments of the prefixes s[1..i] and t[1..j] into 3 types
WsAffine Weight Model
This model has a natural explanation as a finite state automata
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
→ Different tools and DBs to allow biologists a rich suite of queries