Why it matters

SW is foundational local alignment. Understanding shapes bio DP.

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The architecture

DP with zero floor.

Track max cell.

Backtrack until zero.

Smith-Waterman flowDP with zero floorreset negativeTrack max cellstart pointBacktrack to zerolocal alignmentSmith + Waterman 1981; SIMD accelerated versions (SSW) widespread; BLAST heuristic
Smith-Waterman.
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How it works end to end

Zero floor allows local.

SIMD implementations fast.

BLAST heuristic approximation.