Parasail: SIMD C library for global, semi-global, and local pairwise sequence alignments

Daily, Jeffrey A.

doi:10.1186/s12859-016-0930-z

Parasail: SIMD C library for global, semi-global, and local pairwise sequence alignments

Journal Article · Tue Feb 09 23:00:00 EST 2016 · BMC Bioinformatics

DOI:https://doi.org/10.1186/s12859-016-0930-z· OSTI ID:1243170

Daily, Jeffrey A. ^[1]

Pacific Northwest National Lab. (PNNL), Richland, WA (United States)

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. As a result, a faster intra-sequence pairwise alignment implementation is described and benchmarked. 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 12-core processor system, the highest reported for an implementation based on Farrar’s ’striped’ approach. When using only a single thread, parasail was 1.7 times faster than Rognes’s SWIPE. For many score matrices, parasail is faster than BLAST. 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. In conclusion, 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.

View Accepted Manuscript (DOE)

Research Organization:: Pacific Northwest National Laboratory (PNNL), Richland, WA (United States)

Sponsoring Organization:: USDOE

Grant/Contract Number:: AC05-76RL01830

OSTI ID:: 1243170

Report Number(s):: PNNL-SA--114370

Journal Information:: BMC Bioinformatics, Journal Name: BMC Bioinformatics Vol. 17; ISSN 1471-2105

Publisher:: BioMed CentralCopyright Statement

Country of Publication:: United States

Language:: English

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97 MATHEMATICS AND COMPUTING
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Parasail: SIMD C library for global, semi-global, and local pairwise sequence alignments [Supplemental Data] Daily, Jeff https://doi.org/10.6084/m9.figshare.c.3605888 The current record is supplemented by this dataset	dataset	February 2016
Parasail: SIMD C library for global, semi-global, and local pairwise sequence alignments [Supplemental Data] Daily, Jeff https://doi.org/10.6084/m9.figshare.c.3605888.v1 The current record is supplemented by this code	code	February 2016
Additional file 1 of Parasail: SIMD C library for global, semi-global, and local pairwise sequence alignments Daily, Jeff https://doi.org/10.6084/m9.figshare.c.3605888_d1 The current record is supplemented by this dataset	dataset	January 2016
Additional file 1 of Parasail: SIMD C library for global, semi-global, and local pairwise sequence alignments Daily, Jeff https://doi.org/10.6084/m9.figshare.c.3605888_d1.v1 The current record is supplemented by this code	code	February 2016

Parasail: SIMD C library for global, semi-global, and local pairwise sequence alignments

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