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Comput Biol Med. 2013 May;43(4):350-61. doi: 10.1016/j.compbiomed.2012.12.009. Epub 2013 Feb 14.

A data parallel strategy for aligning multiple biological sequences on multi-core computers.

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  • 1College of Information Science and Engineering, Hunan University, Changsha, Hunan 410082, China.


In this paper, we address the large-scale biological sequence alignment problem, which has an increasing demand in computational biology. We employ data parallelism paradigm that is suitable for handling large-scale processing on multi-core computers to achieve a high degree of parallelism. Using the data parallelism paradigm, we propose a general strategy which can be used to speed up any multiple sequence alignment method. We applied five different clustering algorithms in our strategy and implemented rigorous tests on an 8-core computer using four traditional benchmarks and artificially generated sequences. The results show that our multi-core-based implementations can achieve up to 151-fold improvements in execution time while losing 2.19% accuracy on average. The source code of the proposed strategy, together with the test sets used in our analysis, is available on request.

Copyright © 2013 Elsevier Ltd. All rights reserved.

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