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Nat Methods. 2015 Jan;12(1):59-60. doi: 10.1038/nmeth.3176. Epub 2014 Nov 17.

Fast and sensitive protein alignment using DIAMOND.

Author information

1
Department of Computer Science and Center for Bioinformatics, University of Tübingen, Tübingen, Germany.
2
1] Singapore Centre on Environmental Life Sciences Engineering, School of Biological Sciences, Nanyang Technological University, Singapore. [2] Life Sciences Institute, National University of Singapore, Singapore.
3
1] Department of Computer Science and Center for Bioinformatics, University of Tübingen, Tübingen, Germany. [2] Singapore Centre on Environmental Life Sciences Engineering, School of Biological Sciences, Nanyang Technological University, Singapore.

Abstract

The alignment of sequencing reads against a protein reference database is a major computational bottleneck in metagenomics and data-intensive evolutionary projects. Although recent tools offer improved performance over the gold standard BLASTX, they exhibit only a modest speedup or low sensitivity. We introduce DIAMOND, an open-source algorithm based on double indexing that is 20,000 times faster than BLASTX on short reads and has a similar degree of sensitivity.

PMID:
25402007
DOI:
10.1038/nmeth.3176
[Indexed for MEDLINE]
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