We found a match
Your institution may have rights to this item. Sign in to continue.
- Title
AC-DIAMOND v1: accelerating large-scale DNA–protein alignment.
- Authors
Mai, Huijun; Li, Dinghua; Ting, Hing-Fung; Zhang, Yifan; Wong, Chi-Kwong; Leung, Henry Chi-Ming; Luo, Ruibang; Lam, Tak-Wah
- Abstract
Summary AC-DIAMOND (v1) is a DNA–protein alignment tool designed to tackle the efficiency challenge of aligning large amount of reads or contigs to protein databases. When compared with the previously most efficient method DIAMOND, AC-DIAMOND gains a 6- to 7-fold speed-up, while retaining a similar degree of sensitivity. The improvement is rooted at two aspects: first, using a compressed index of seeds with adaptive-length to speed-up the matching between query and reference sequences; second, adopting a compact form of dynamic programing to fully utilize the parallelism of the SIMD capability. Availability and implementation Software source codes and binaries available at https://github.com/Maihj/AC-DIAMOND/ Supplementary information Supplementary data are available at Bioinformatics online.
- Subjects
DNA-protein interactions; PROTEIN analysis; SOURCE code; NUCLEOTIDE sequencing; DYNAMIC programming
- Publication
Bioinformatics, 2018, Vol 34, Issue 21, p3744
- ISSN
1367-4803
- Publication type
Article
- DOI
10.1093/bioinformatics/bty391