BLAST Seed-and-Extend Aligner

Query vs. Database

Seeding & Extension

Word size k 6

Mismatch penalty 3

X-drop threshold 8

Live Readouts

Seeds found

Best score

Best local alignment

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Single-letter dot-plot match Exact word (seed), length k Best extended local alignment

How it works

BLAST never runs full dynamic-programming alignment (Needleman–Wunsch / Smith–Waterman) over the whole query × database matrix — that would be too slow at genome scale. Instead it uses a three-stage heuristic:

1. SEED    index all length-k substrings ("words") of the query;
           scan the database for exact k-length matches → anchor points
2. EXTEND  from each seed, walk outward along its diagonal, adding
           match score (+m) or mismatch penalty (−p) at each step
3. X-DROP  stop extending once the running score falls more than X
           below the best score seen so far on that diagonal:
             stop when  bestSoFar − current(t) > X
           then trim the alignment back to the point of bestSoFar

Only diagonals that contain at least one exact seed are ever extended — this is what makes BLAST fast: it prunes the search from O(query·database) full alignment down to a handful of promising diagonals.

Word size k — shorter words seed more often (more sensitive, slower in real BLAST); longer words seed rarely but only on strong homology.
Mismatch penalty — how sharply a mismatched base pulls the running score down during extension (match is fixed at +1).
X-drop threshold — how far the score is allowed to dip below its running best before extension gives up; larger X tolerates longer stretches of mismatches inside one alignment.

The database sequence here is built by taking a chunk of the query, mutating roughly 15% of its bases, and burying it inside random flanking DNA — exactly the kind of divergent homolog BLAST is designed to find. The gold bars mark the single best-scoring diagonal after seed-and-extend, i.e. the local alignment BLAST would report.

X → database position Z → query position Y → cumulative extension score

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