skip to main content
OSTI.GOV title logo U.S. Department of Energy
Office of Scientific and Technical Information

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 » local alignments are available in a stand-alone C library.« less

Authors:
 [1]
  1. Pacific Northwest National Lab. (PNNL), Richland, WA (United States)
Publication Date:
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:
Journal Article: 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.
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.
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.
@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 = {Wed Feb 10 00:00:00 EST 2016},
month = {Wed Feb 10 00:00:00 EST 2016}
}

Journal Article:
Free Publicly Available Full Text
Publisher's Version of Record

Citation Metrics:
Cited by: 3 works
Citation information provided by
Web of Science

Save / Share:

Works referenced in this record:

Basic local alignment search tool
journal, October 1990

  • Altschul, Stephen F.; Gish, Warren; Miller, Webb
  • Journal of Molecular Biology, Vol. 215, Issue 3, p. 403-410
  • DOI: 10.1016/S0022-2836(05)80360-2

Amino acid substitution matrices from protein blocks.
journal, November 1992

  • Henikoff, S.; Henikoff, J. G.
  • Proceedings of the National Academy of Sciences, Vol. 89, Issue 22, p. 10915-10919
  • DOI: 10.1073/pnas.89.22.10915