Muhammad Shoaib

Pruning the Search, Not the Signal: Adaptive-Banding Needleman–Wunsch via Protein Language Model Confidence

Dynamic programming (DP) yields exact quadratic-time (O(NM)) pairwise sequence alignments. Static banding heuristics (O(NW)) fail catastrophically on low-identity (< 30%), asymmetric insertions/deletions (indels), or extreme length ratios, dropping core-block Sum-of-Pairs (SP) score recovery to 20%– 50%. Conversely, re...