The enormous growth of biological sequence databases has caused bioinformatics to be rapidly moving towards a data-intensive, computational science. As a result, the computational power needed by bioinformatics applications is growing rapidly as well. The recent emergence of low cost parallel multicore accelerator technologies has made it possible to reduce execution times of many bioinformatics applications. In this paper, we demonstrate how the Cell Broadband Engine can be used as a computational platform to accelerate two approaches for protein sequence database scanning: exhaustive and heuristic. We present efficient parallelization techniques for two representative algorithms: the dynamic programming based Smith–Waterman algorithm and the popular BLASTP heuristic. Their implementation on a Playstation®3 leads to significant runtime savings compared to corresponding sequential implementations.

中文翻译：

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细胞宽带引擎上的高性能蛋白质序列数据库扫描

生物序列数据库的巨大发展已导致生物信息学迅速走向数据密集型计算科学。结果，生物信息学应用程序所需的计算能力也在迅速增长。低成本并行多核加速器技术的最新出现使得减少许多生物信息学应用程序的执行时间成为可能。在本文中，我们演示了细胞宽带引擎如何用作计算平台来加速蛋白质序列数据库扫描的两种方法：穷举法和启发式法。我们为两种代表性算法提供了有效的并行化技术：基于Smith-Waterman算法的动态编程和流行的BLASTP启发式算法。