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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Cited by: 3 works

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Table 1: Software included in performance testing

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Works referenced in this record:

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journal, May 2015

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Works referencing / citing this record:

Introducing difference recurrence relations for faster semi-global alignment of long sequences
journal, February 2018

Suzuki, Hajime; Kasahara, Masahiro
BMC Bioinformatics, Vol. 19, Issue S1
DOI: 10.1186/s12859-018-2014-8

Deciphering highly similar multigene family transcripts from Iso-Seq data with IsoCon
journal, November 2018

Sahlin, Kristoffer; Tomaszkiewicz, Marta; Makova, Kateryna D.
Nature Communications, Vol. 9, Issue 1
DOI: 10.1038/s41467-018-06910-x

Introducing difference recurrence relations for faster semi-global alignment of long sequences
journal, February 2018

Suzuki, Hajime; Kasahara, Masahiro
BMC Bioinformatics, Vol. 19, Issue S1
DOI: 10.1186/s12859-018-2014-8

A review of alignment based similarity measures for web usage mining
journal, May 2019

Luu, Vinh-Trung; Forestier, Germain; Weber, Jonathan
Artificial Intelligence Review, Vol. 53, Issue 3
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SWIMM 2.0: Enhanced Smith–Waterman on Intel’s Multicore and Manycore Architectures Based on AVX-512 Vector Extensions
journal, July 2018

Rucci, Enzo; Garcia Sanchez, Carlos; Botella Juan, Guillermo
International Journal of Parallel Programming, Vol. 47, Issue 2
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Edlib: a C/C ++ library for fast, exact sequence alignment using edit distance
journal, January 2017

Šošić, Martin; Šikić, Mile
Bioinformatics, Vol. 33, Issue 9
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Minimap2: pairwise alignment for nucleotide sequences
journal, May 2018

Li, Heng
Bioinformatics, Vol. 34, Issue 18
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Figures / Tables found in this record:

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Other research related to this record:

Additional file 1 of Parasail: SIMD C library for global, semi-global, and local pairwise sequence alignments
code, February 2016

Daily, Jeff
figshare-Supplementary information for journal article at DOI: 10.1186/s12859-016-0930-z, 1 GZ file (1.19 MB)
DOI: 10.6084/m9.figshare.c.3605888_d1.v1
This code is a supplement to the current record