Accelign: a GPU-based library for accelerating pairwise sequence alignment
Felix Kallenborn, Fawaz Dabbaghie, Martin Steinegger, Bertil Schmidt · 2026
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Description
Felix Kallenborn, Fawaz Dabbaghie, Martin Steinegger, and Bertil Schmidt present a 2026 software library called Accelign for fast sequence alignment on graphics cards. Pairwise alignment matches DNA, RNA, or protein letters and sits inside many biology pipelines, but its cost grows steeply with sequence length. Faster code on modern chips can cut total pipeline time a great deal.
Accelign uses a shared wavefront design that adapts to local, global, and semi-global alignment with common scoring rules. It handles one-to-one, one-to-many, and all-to-all jobs for genome and protein data alike. Peak speeds beat many prior central and graphics tools in real cases cited. Speed also scales in a straight line as more graphics cards are added.
Catalog record
| CREATOR | Felix Kallenborn, Fawaz Dabbaghie, Martin Steinegger, Bertil Schmidt |
|---|---|
| YEAR | 2026 |
| COLLECTION | PAPERS |
| FORMAT | TXT |
| FILE SIZE | 148202 |
| LICENSE | https://creativecommons.org/licenses/by/4.0 |
| RIGHTS | CC BY |
| SOURCE | Europe PMC |