Parasail: SIMD C library for global, semi-global, and local pairwise sequence alignments.
Parasail: SIMD C library for global, semi-global, and local pairwise sequence alignments.
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DOI：
10.1186/s12859-016-0930-z
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发表时间：
2016-02-10
影响因子：
3
通讯作者：
Daily J
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文献类型：
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作者：
Daily J
序列比对算法是许多生物信息学应用的关键组成部分。虽然已经为x86 cpu开发了各种快速Smith-Waterman本地序列对齐实现，但大多数都嵌入到较大的数据库搜索工具中。此外，Needleman-Wunsch全局序列比对及其半全局变体的快速实现并不广泛。本文介绍了第一个用于本地、全局和半全局成对序列内对齐的软件库，并改进了以前的序列内实现的性能。描述了一种更快的序列内局部成对比对实现，并对其进行了基准测试，包括新的全局和半全局变体。使用375个残差查询序列，在双Intel Xeon E5-2670 24核处理器系统上实现了每秒1360亿个单元更新（GCUPS）的速度，这是基于Farrar的“条纹”方法实现的最高速度。Rognes的SWIPE最优数据库搜索应用程序通常仍然是最快的，对于短于500个氨基酸的序列，它比Parasail快1.2到至多2.4倍。然而，Parasail在较长的序列中速度更快。对于全局对齐，Parasail的前缀扫描实现通常是最快的，甚至比Farrar的“条纹”方法还快，但是opal库对于单线程应用程序更快。该软件库设计用于64位Linux、OS X或Windows上的SSE2、SSE41或AVX2处理器。源代码在Battelle bsd风格许可下可从https://github.com/jeffdaily/parasail获得。需要最佳对齐分数的应用程序可以从改进的性能中受益。SIMD全局、半全局和局部对齐第一次在独立的C库中可用。本文的在线版本（doi:10.1186/s12859-016-0930-z）包含补充材料，授权用户可以使用。
Sequence alignment algorithms are a key component of many bioinformatics applications. Though various fast Smith-Waterman local sequence alignment implementations have been developed for x86 CPUs, most are embedded into larger database search tools. In addition, fast implementations of Needleman-Wunsch global sequence alignment and its semi-global variants are not as widespread. This article presents the first software library for local, global, and semi-global pairwise intra-sequence alignments and improves the performance of previous intra-sequence implementations. A faster intra-sequence local pairwise alignment implementation is described and benchmarked, including new global and semi-global variants. Using a 375 residue query sequence a speed of 136 billion cell updates per second (GCUPS) was achieved on a dual Intel Xeon E5-2670 24-core processor system, the highest reported for an implementation based on Farrar’s ‘striped’ approach. Rognes’s SWIPE optimal database search application is still generally the fastest available at 1.2 to at best 2.4 times faster than Parasail for sequences shorter than 500 amino acids. However, Parasail was faster for longer sequences. For global alignments, Parasail’s prefix scan implementation is generally the fastest, faster even than Farrar’s ‘striped’ approach, however the opal library is faster for single-threaded applications. The software library is designed for 64 bit Linux, OS X, or Windows on processors with SSE2, SSE41, or AVX2. Source code is available from https://github.com/jeffdaily/parasail under the Battelle BSD-style license. Applications that require optimal alignment scores could benefit from the improved performance. For the first time, SIMD global, semi-global, and local alignments are available in a stand-alone C library. The online version of this article (doi:10.1186/s12859-016-0930-z) contains supplementary material, which is available to authorized users.