AC-DIAMOND v1: accelerating large-scale DNA-protein alignment.
basic_science · Level V
Where this comes from
- Record sourced from PubMed, PMID 29771282.
- Also identified by DOI 10.1093/bioinformatics/bty391.
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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.
Medical subject headings
- Software