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Parallel Genomic Alignments on the Cell Broadband Engine

机译：细胞宽带引擎上的平行基因组比对

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摘要

Genomic alignments, as a means to uncover evolutionary relationships among organisms, are a fundamental tool in computational biology. There is considerable recent interest in using the Cell Broadband Engine, a heterogeneous multicore chip that provides high performance, for biological applications. However, work in genomic alignments so far has been limited to computing optimal alignment scores using quadratic space for the basic global/local alignment problem. In this paper, we present a comprehensive study of developing alignment algorithms on the Cell, exploiting its thread and data level parallelism features. First, we develop a parallel implementation on the Cell that computes optimal alignments and adopts Hirschberg''s linear space technique. The former is essential, as merely computing optimal alignment scores is not useful, while the latter is needed to permit alignments of longer sequences. We then present Cell implementations of two advanced alignment techniquesȁ4;spliced alignments and syntenic alignments. Spliced alignments are useful in aligning mRNA sequences with corresponding genomic sequences to uncover the gene structure. Syntenic alignments are used to discover conserved exons and other sequences between long genomic sequences from different organisms. We present experimental results for these three types of alignments on 16 Synergistic Processing Elements of the IBM QS20 dual-Cell blade system.
机译：基因组比对，作为揭示生物之间进化关系的一种手段，是计算生物学的基本工具。最近，人们对将Cell Broadband Engine（一种具有高性能的异构多核芯片）用于生物学应用感兴趣。但是，到目前为止，基因组比对的工作仅限于使用平方空间计算基本整体/局部比对问题的最佳比对分数。在本文中，我们对利用Cell的线程和数据级别并行性功能开发基于Cell的对齐算法进行了全面的研究。首先，我们在Cell上开发了并行实现，该实现可计算最佳对齐方式并采用Hirschberg的线性空间技术。前者是必不可少的，因为仅计算最佳比对得分是没有用的，而后者则需要允许较长序列的比对。然后，我们介绍两种先进的比对技术ȁ4的Cell实现：拼接比对和同义比对。剪接的比对可用于使mRNA序列与相应的基因组序列比对以揭示基因结构。序列比对用于发现来自不同生物体的长基因组序列之间的保守外显子和其他序列。我们在IBM QS20双电池刀片系统的16个协同处理元件上呈现这三种类型的比对的实验结果。

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