GPU-BLAST：利用图形处理器加速蛋白质序列比对。

GPU-BLAST: using graphics processors to accelerate protein sequence alignment.

机构信息

Department of Chemical Engineering, Carnegie Mellon University, Pittsburgh, PA 15213, USA.

出版信息

Bioinformatics. 2011 Jan 15;27(2):182-8. doi: 10.1093/bioinformatics/btq644. Epub 2010 Nov 18.

DOI:10.1093/bioinformatics/btq644

PMID:21088027

原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC3018811/

Abstract

MOTIVATION

The Basic Local Alignment Search Tool (BLAST) is one of the most widely used bioinformatics tools. The widespread impact of BLAST is reflected in over 53,000 citations that this software has received in the past two decades, and the use of the word 'blast' as a verb referring to biological sequence comparison. Any improvement in the execution speed of BLAST would be of great importance in the practice of bioinformatics, and facilitate coping with ever increasing sizes of biomolecular databases.

RESULTS

Using a general-purpose graphics processing unit (GPU), we have developed GPU-BLAST, an accelerated version of the popular NCBI-BLAST. The implementation is based on the source code of NCBI-BLAST, thus maintaining the same input and output interface while producing identical results. In comparison to the sequential NCBI-BLAST, the speedups achieved by GPU-BLAST range mostly between 3 and 4.

AVAILABILITY

The source code of GPU-BLAST is freely available at http://archimedes.cheme.cmu.edu/biosoftware.html.

摘要

动机

基本局部比对搜索工具（BLAST）是最广泛使用的生物信息学工具之一。BLAST 的广泛影响体现在过去 20 年中该软件获得的超过 53000 次引用，以及“blast”一词作为动词用于指代生物序列比较。BLAST 执行速度的任何提高在生物信息学实践中都非常重要，并有助于应对不断增大的生物分子数据库。