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RNA Structure Alignment on a Massively Parallel Computer

机译：RNA结构对准在大型平行计算机上

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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架构上有效地实现了COVE软件套件，使得使用COVE实用用于扫描属于已知RNA家族的新基因的大型生物信息学数据库。使用协方差模型，扫描数据库序列以匹配与给定系列的共识RNA二级结构和序列匹配的子序列。通过在Maspar处理器阵列的行中并行分析数据库序列并将三维动态评分编程矩阵映射到每行上的数据库序列来实现巨大的并行性。我们对TRNA和SRP-RNA进行了Genbank和Nematode基因组序列的扫描，具有成功的结果。并行实现实现了两个数量级的加速度，使数据库搜索时间从几天到几天。我们认为这是RNA分析的有用进展。我们希望通过算法和实现优化进一步减少仍然需要的时间，以便可以广泛且容易地使用COVE。

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