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. 2018 Nov 1;34(21):3744-3746.
doi: 10.1093/bioinformatics/bty391.

AC-DIAMOND v1: Accelerating Large-Scale DNA-protein Alignment

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AC-DIAMOND v1: Accelerating Large-Scale DNA-protein Alignment

Huijun Mai et al. Bioinformatics. .

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.

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