TSTA: thread and SIMD-based trapezoidal pairwise/multiple sequence-alignment method
Peiyu Zong, Wenpeng Deng, Jian Liu, Jue Ruan, zong peiyu, Scott Edmunds, Hongfang Zhang, Christopher Hunter, Xingbao Song, Yuansheng Liu, Hongfang Zhang, zong peiyu, Hongfang Zhang, Yuansheng Liu, Hongfang Zhang, zong peiyu, Hongfang Zhang, Yuansheng Liu, Hongfang Zhang, zong peiyu, Hongfang Zhang, · 2024
Read TSTA: thread and SIMD-based trapezoidal pairwise/multiple sequence-alignment method by Peiyu Zong, Wenpeng Deng, Jian Liu, Jue Ruan, zong peiyu, Scott Edmunds, Hongfang Zhang, Christopher Hunter, Xingbao Song, Yuansheng Liu, Hongfang Zhang, zong peiyu, Hongfang Zhang, Yuansheng Liu, Hongfang Zhang, zong peiyu, Hongfang Zhang, Yuansheng Liu, Hongfang Zhang, zong peiyu, Hongfang Zhang, (2024) in the Tower of Babel, a free online library of public-domain works preserved in clean, searchable text. No sign-up. The full text is served as a plain-text file at a predictable URL, where text is present: https://antarctic-labs.com/tower-of-babel/pmc-11558659.txt.
Description
Aligning DNA sequences is a workhorse computation that long modern reads have made painfully slow. Peiyu Zong and co-authors speed it up in a 2024 paper with an algorithm that splits the work across processor cores and vector units at once.
The classic method fills a scoring grid cell by cell, which wastes effort on regions that cannot matter. Their trapezoidal variant narrows the computed region while leaning on thread parallelism and single-instruction tricks. It handles both pairwise alignment and the harder multiple-sequence version. The code is public, so labs can drop it into existing pipelines. Speed of this kind quietly decides how much sequencing a small team can afford to analyze.
Catalog record
| CREATOR | Peiyu Zong, Wenpeng Deng, Jian Liu, Jue Ruan, zong peiyu, Scott Edmunds, Hongfang Zhang, Christopher Hunter, Xingbao Song, Yuansheng Liu, Hongfang Zhang, zong peiyu, Hongfang Zhang, Yuansheng Liu, Hongfang Zhang, zong peiyu, Hongfang Zhang, Yuansheng Liu, Hongfang Zhang, zong peiyu, Hongfang Zhang, |
|---|---|
| YEAR | 2024 |
| COLLECTION | PAPERS |
| FORMAT | TXT |
| FILE SIZE | 48 KB |
| VERSION | 1.0 |
| LICENSE | CC BY 4.0 |
| RIGHTS | CC BY |
| SOURCE | Europe PMC |