使用 DIAMOND 进行快速灵敏的蛋白质比对。

Fast and sensitive protein alignment using DIAMOND.

机构信息

Department of Computer Science and Center for Bioinformatics, University of Tübingen, Tübingen, Germany.

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.

出版信息

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

DOI:10.1038/nmeth.3176

PMID:25402007

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.

摘要

将测序reads 与蛋白质参考数据库比对是宏基因组学和数据密集型进化项目中的主要计算瓶颈。尽管最近的工具在性能上优于标准的 BLASTX，但它们的加速效果只是略有提高或灵敏度较低。我们引入了 DIAMOND，这是一种基于双索引的开源算法，在短读长上比 BLASTX 快 20000 倍，并且具有相似的灵敏度。