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

doi:10.1186/s12859-016-0930-z

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

Abstract

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, andmore »« less

Authors:

Daily, Jeffrey A. ^[1]

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

Publication Date:: 2016-02-10

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

Sponsoring Org.:: USDOE

OSTI Identifier:: 1243170

Report Number(s):: PNNL-SA-114370
Journal ID: ISSN 1471-2105

Grant/Contract Number:: AC05-76RL01830

Resource Type:: Accepted Manuscript

Journal Name:: BMC Bioinformatics

Additional Journal Information:: Journal Volume: 17; Journal ID: ISSN 1471-2105

Publisher:: BioMed Central

Country of Publication:: United States

Language:: English

Subject:: 97 MATHEMATICS AND COMPUTING; Smith-Waterman; Needleman-Wunsch; semi-global alignment; sequence alignment; SIMD; database search

Citation Formats


                    Daily, Jeffrey A. Parasail: SIMD C library for global, semi-global, and local pairwise sequence alignments.  United States: N. p., 2016. 
        Web.  doi:10.1186/s12859-016-0930-z.

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                    Daily, Jeffrey A. Parasail: SIMD C library for global, semi-global, and local pairwise sequence alignments.  United States.  doi:10.1186/s12859-016-0930-z.

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                    Daily, Jeffrey A. Wed .  
        "Parasail: SIMD C library for global, semi-global, and local pairwise sequence alignments".  United States.  doi:10.1186/s12859-016-0930-z.  https://www.osti.gov/servlets/purl/1243170.

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@article{osti_1243170,

  title        = {Parasail: SIMD C library for global, semi-global, and local pairwise sequence alignments},

  author       = {Daily, Jeffrey A.},

  abstractNote = {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.},

  doi          = {10.1186/s12859-016-0930-z},

  journal      = {BMC Bioinformatics},

  number       = ,

  volume       = 17,

  place        = {United States},

  year         = {2016},

  month        = {2}

}

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DOI: 10.1186/s12859-016-0930-z

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Table 1: Software included in performance testing

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Works referenced in this record:

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Rognes, T.; Seeberg, E.
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Rognes, Torbjørn
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SSW Library: An SIMD Smith-Waterman C/C++ Library for Use in Genomic Applications
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Zhao, Mengyao; Lee, Wan-Ping; Garrison, Erik P.
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A work stealing based approach for enabling scalable optimal sequence homology detection
journal, May 2015

Daily, Jeff; Kalyanaraman, Ananth; Krishnamoorthy, Sriram
Journal of Parallel and Distributed Computing, Vol. 79-80
DOI: 10.1016/j.jpdc.2014.08.009

Figures / Tables found in this record:

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