Author

Waqas Ali

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Open access Sep 2026

A Scalable Distributed-Memory MPI Implementation of Smith-Waterman with Token-Passing Traceback

As genomic sequencing produces increasingly massive datasets, accurate local sequence alignment via the Smith-Waterman(SW) algorithm remains computationally prohibitive due to its space and quadratic time complexity O(mn). While parallelization addresses a path forward, existing MPI-based solutions present a critical b...

Maryam Fatima, Waqas Ali · bioRxiv · 0 citations

Open access Aug 2026

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...

Muhammad Shoaib, Waqas Ali · bioRxiv · 0 citations