AC-DIAMOND: Accelerating Protein Alignment via Better SIMD Parallelization and Space-Efficient Indexing

Conference paper
Part of the Lecture Notes in Computer Science book series (LNCS, volume 9656)


To speed up the alignment of DNA reads or assembled contigs against a protein database has been a challenge up to now. The recent tool DIAMOND has significantly improved the speed of BLASTX and RAPSearch, while giving similar degree of sensitivity. Yet for applications like metagenomics, where large amount of data is involved, DIAMOND still takes a lot of time. This paper introduces an even faster protein alignment tool, called AC-DIAMOND, which attempts to speed up DIAMOND via better SIMD parallelization and more space-efficient indexing of the reference database; the latter allows more queries to be loaded into the memory and processed together. Experimental results show that AC-DIAMOND is about 4 times faster than DIAMOND on aligning DNA reads or contigs, while retaining the same sensitivity as DIAMOND.For example, the latest assembly of the Iowa praire soil metagenomic dataset generates over 9 milllion of contigs, with a total size about 7 Gbp; when aligning these contigs to the protein database NCBI-nr, DIAMOND takes 4 to 5 days, and AC-DIAMOND takes about 1 day. AC-DIAMOND is available for testing at


DNA-protein alignment SIMD Dynamic programming Compressed indexing 


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Copyright information

© Springer International Publishing Switzerland 2016

Authors and Affiliations

  1. 1.HKU-BGI Bioinformatics Algorithms and Core Technology Laboratory, Department of Computer ScienceUniversity of Hong KongHong KongChina
  2. 2.L3 Bioinformatics LimitedHong KongChina
  3. 3.United Electronics Co., LtdBeijingChina

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