BLAST Seed-and-Extend Dot-Plot (2D)

This simulator renders the same BLAST (Basic Local Alignment Search Tool) seed-and-extend heuristic behind essentially every "find this sequence in a genome" search, as a classic 2D dot-plot you can pan and zoom, paired with a live line chart of the running extension score. A short query DNA sequence is compared against a longer database sequence (containing a mutated, embedded copy of part of the query): 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 with match/mismatch scoring and X-drop pruning. The score-trace panel plots that running score explicitly, shading the X-drop tolerance band so you can see exactly where and why extension would stop. Adjustable word size, match score, mismatch penalty and X-drop threshold, plus live seed counts, best-score and stop-count readouts, show how BLAST trades sensitivity for the speed that makes genome-scale search possible.