bioRxiv / medRxiv
open access
Pruning the Search, Not the Signal: Adaptive-Banding Needleman-Wunsch Sequence Alignment 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%-5
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