Bioinformatics: Sequence Alignment DP-Matrix Explorer

Bioinformatics turns biological sequences into problems that dynamic programming can solve exactly. This simulator generates two short DNA sequences — one a mutated copy of the other — and builds the Needleman-Wunsch global-alignment score matrix between them cell by cell. Rendered as a 3D landscape, each cell's height is its dynamic-programming score, and the bright ridge traces the optimal path back through the matrix that recovers the actual best alignment. Adjust sequence length, mutation rate, mismatch penalty and gap penalty to see how the landscape reshapes and how the traceback path bends toward gaps or mismatches.