Parasail: SIMD C library for global, semi-global, and local pairwise sequence alignments
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 »
- Authors:
-
[1]
- Pacific Northwest National Lab. (PNNL), Richland, WA (United States)
- Publication Date:
- Report Number(s):
- PNNL-SA-114370
Journal ID: ISSN 1471-2105
- Grant/Contract Number:
- AC05-76RL01830
- Type:
- Accepted Manuscript
- Journal Name:
- BMC Bioinformatics
- Additional Journal Information:
- Journal Volume: 17; Journal ID: ISSN 1471-2105
- Publisher:
- BioMed Central
- Research Org:
- Pacific Northwest National Lab. (PNNL), Richland, WA (United States)
- Sponsoring Org:
- USDOE
- Country of Publication:
- United States
- Language:
- English
- Subject:
- 97 MATHEMATICS AND COMPUTING; Smith-Waterman; Needleman-Wunsch; semi-global alignment; sequence alignment; SIMD; database search
- OSTI Identifier:
- 1243170
- Free Publicly Accessible Full Text
-
Accepted Manuscript (DOE)
- Publisher's Version of Record
- https://doi.org/10.1186/s12859-016-0930-z