Fast and sensitive protein alignment using DIAMOND.

Nat Methods 2015 Jan 17;12(1):59-60. Epub 2014 Nov 17.

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.

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.

Download full-text PDF

Source
http://dx.doi.org/10.1038/nmeth.3176DOI Listing
January 2015
23 Reads

Publication Analysis

Top Keywords

tools offer
4
indexing 20000
4
offer improved
4
double indexing
4
improved performance
4
projects tools
4
evolutionary projects
4
times faster
4
metagenomics data-intensive
4
diamond open-source
4
20000 times
4
performance gold
4
based double
4
speedup low
4
open-source algorithm
4
low sensitivity
4
sensitivity introduce
4
introduce diamond
4
modest speedup
4
exhibit modest
4

References

(Supplied by CrossRef)

J Handelsman et al.
Chem. Biol. 1998

DA Benson et al.
Nucleic Acids Res. 2005

M Kanehisa et al.
Nucleic Acids Res. 2000

SF Altschul et al.
J. Mol. Biol. 1990

WJ Kent et al.
Genome Res. 2002

RC Edgar et al.
Bioinformatics 2010

Y Zhao et al.
Bioinformatics 2012

DH Huson et al.
Bioinformatics 2014

S Burkhardt et al.
Fundamenta Informaticae 2003

B Ma et al.
Bioinformatics 2002

L Ilie et al.
BMC Genomics 2011

Similar Publications