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

Bioinformatics
Huijun MaiTak-Wah Lam

Abstract

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. Software source codes and binaries available at https://github.com/Maihj/AC-DIAMOND/. Supplementary data are available at Bioinformatics online.

References

Oct 5, 1990·Journal of Molecular Biology·S F AltschulD J Lipman
Mar 19, 2014·Proceedings of the National Academy of Sciences of the United States of America·Adina Chuang HoweC Titus Brown
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Oct 17, 2017·Nature Biotechnology·Martin Steinegger, Johannes Söding

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Citations

Dec 23, 2020·BMC Genomics·Chi-Ming LeungTak-Wah Lam

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