AC-DIAMOND v1: accelerating large-scale DNA–protein alignment | Zendy

Huijun Mai | Zendy; Yifan Zhang | Zendy; Dinghua Li | Zendy; Henry Chi-Ming Leung | Zendy; Ruibang Luo | Zendy; Chi-Kwong Wong | Zendy; HingFung Ting | Zendy; TakWah Lam | Zendy

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AC-DIAMOND v1: accelerating large-scale DNA–protein alignment

Author(s) -

Huijun Mai,

Yifan Zhang,

Dinghua Li,

Henry Chi-Ming Leung,

Ruibang Luo,

Chi-Kwong Wong,

HingFung Ting,

TakWah Lam

Publication year - 2018

Publication title -

bioinformatics

Language(s) - English

Resource type - Journals

SCImago Journal Rank - 3.599

H-Index - 390

eISSN - 1367-4811

pISSN - 1367-4803

DOI - 10.1093/bioinformatics/bty391

Subject(s) - computer science , simd , diamond , contig , matching (statistics) , software , parallel computing , slicing , parallelism (grammar) , sensitivity (control systems) , computational science , programming language , computer graphics (images) , electronic engineering , mathematics , materials science , chemistry , engineering , biochemistry , statistics , genome , composite material , gene

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.

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