Fast and sensitive protein alignment using DIAMOND

被引：8115

作者：

Buchfink, Benjamin ^{[1
,2
]}

Xie, Chao ^{[3
,4
]}

Huson, Daniel H. ^{[1
,2
,3
]}

机构：

[1] Univ Tubingen, Dept Comp Sci, Tubingen, Germany

[2] Univ Tubingen, Ctr Bioinformat, Tubingen, Germany

[3] Nanyang Technol Univ, Sch Biol Sci, Singapore Ctr Environm Life Sci Engn, Singapore 639798, Singapore

[4] Natl Univ Singapore, Inst Life Sci, Singapore 117548, Singapore

来源：

NATURE METHODS | 2015年 / 12卷 / 01期

基金：

新加坡国家研究基金会;

关键词：

SEARCH;

D O I：

10.1038/nmeth.3176

中图分类号：

Q5 [生物化学];

学科分类号：

071010 ; 081704 ;

摘要：

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.

引用

页码：59 / 60

页数：2

共 18 条

[1] BASIC LOCAL ALIGNMENT SEARCH TOOL
ALTSCHUL, SF
GISH, W
MILLER, W
MYERS, EW
LIPMAN, DJ
[J]. JOURNAL OF MOLECULAR BIOLOGY, 1990, 215 (03) : 403 - 410
[2] Benson DA, 2005, NUCLEIC ACIDS RES, V33, pD34, DOI [10.1093/nar/gki063, 10.1093/nar/gku1216]
[3] Burkhardt S., 2003, Fundamenta informaticae, V23, P1001
[4] Search and clustering orders of magnitude faster than BLAST
Edgar, Robert C.
[J]. BIOINFORMATICS, 2010, 26 (19) : 2460 - 2461
[5] Molecular biological access to the chemistry of unknown soil microbes: A new frontier for natural products
Handelsman, J
Rondon, MR
Brady, SF
Clardy, J
Goodman, RM
[J]. CHEMISTRY & BIOLOGY, 1998, 5 (10): : R245 - R249
[6] A poor man's BLASTX-high-throughput metagenomic protein database search using PAUDA
Huson, Daniel H.
Xie, Chao
[J]. BIOINFORMATICS, 2014, 30 (01) : 38 - 39
[7] Seeds for effective oligonucleotide design
Ilie, Lucian
Ilie, Silvana
Khoshraftar, Shima
Bigvand, Anahita Mansouri
[J]. BMC GENOMICS, 2011, 12
[8] Jansson J., 2011, Microbe Magazine, V6, P309, DOI [DOI 10.1128/MICROBE.6.309, 10.1128/microbe.6.309]
[9] KEGG: Kyoto Encyclopedia of Genes and Genomes
Kanehisa, M
Goto, S
[J]. NUCLEIC ACIDS RESEARCH, 2000, 28 (01) : 27 - 30
[10] Kent WJ, 2002, GENOME RES, V12, P656, DOI [10.1101/gr.229202. Article published online before March 2002, 10.1101/gr.229202]

← 1 2 →