BLAST Seed-and-Extend Aligner

This simulator renders the core heuristic behind BLAST (Basic Local Alignment Search Tool) — the algorithm that powers essentially every "find this sequence in a genome" search in bioinformatics — as a real 3D dot-plot. A short query DNA sequence and a longer database sequence (containing a mutated, embedded copy of part of the query) are compared position by position: single-letter matches form the faint background dot-plot, exact k-length "words" light up as seeds along their diagonal, and the single best-scoring diagonal is extended outward with match/mismatch scoring and X-drop pruning into the gold local alignment BLAST would actually report. Adjustable word size, mismatch penalty and X-drop threshold, plus live seed counts and best-score readouts, show exactly how BLAST trades sensitivity for the speed that makes genome-scale search possible.