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RNA Structure Alignment on a Massively Parallel Computer

机译：大规模并行计算机上的RNA结构比对

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摘要

An efficient implementation of the COVE software suite on the MasPar architecture makes the use of COVE practical for scanning large bioinformatics databases for new genes belonging to known RNA families. Using a covariance model, database sequences are scanned for subsequences that match the consensus RNA secondary structure and sequence of a given family. Massive parallelism has been achieved by analysing database sequences in parallel over the rows of the MasPar processor array and mapping the three-dimensional dynamic scoring programming matrix onto each row. We have carried out scans of GenBank and nematode genome sequence for tRNA and SRP-RNAs with successful results. The parallel implementation achieves speedups of two orders of magnitude, bringing database search times down from months to days. We think this is a useful advance in the analysis of RNA. We hope to reduce the time taken still further by algorithmic and implementation optimisations so that COVE can be widely and easily used.
机译：在MasPar架构上有效地实现COVE软件包的功能，使COVE实用地用于扫描大型生物信息数据库，寻找属于已知RNA家族的新基因。使用协方差模型，扫描数据库序列以查找与给定家族的共有RNA二级结构和序列相匹配的子序列。通过并行分析MasPar处理器阵列的行上的数据库序列并将三维动态评分编程矩阵映射到每一行，可以实现大规模并行性。我们已经对GenBank和线虫基因组序列进行了tRNA和SRP-RNA的扫描，并获得了成功的结果。并行实现可将速度提高两个数量级，从而使数据库搜索时间从数月缩短至数天。我们认为这是在RNA分析中的有用进展。我们希望通过算法和实现优化来减少进一步花费的时间，以使COVE可以广泛且容易地使用。

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  • 来源
  • 会议地点 Milan(IT);Milan(IT)
  • 作者

    Henry Ellingworth; Sean R. Eddy;

  • 作者单位

    MasPar Computer Ltd, 8 Commerce Park, Brunei Road, Theale RG7 4AB UK Fujitsu Systems (Europe), Stockley Park UB11 1AB UK;

    MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 2QH UK Dept. of Genetics, Washington University Medical School, 4566 Scott Ave. Box 8232, St. Louis MO 63110 USA;

  • 会议组织
  • 原文格式 PDF
  • 正文语种 eng
  • 中图分类 TQ4;
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