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首页> 外文期刊>Journal of Bioinformatics and Computational Biology >ON COMPARING TWO STRUCTURED RNA MULTIPLE ALIGNMENTS
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ON COMPARING TWO STRUCTURED RNA MULTIPLE ALIGNMENTS

机译：两种结构化RNA多重对齐方式的比较

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摘要

We present a method, called BlockMatch, for aligning two blocks, where a block is an RNA multiple sequence alignment with the consensus secondary structure of the alignment in Stockholm format. The method employs a quadratic-time dynamic programming algorithm for aligning columns and column pairs of the multiple alignments in the blocks. Unlike many other tools that can perform pairwise alignment of either single sequences or structures only, BlockMatch takes into account the characteristics of all the sequences in the blocks along with their consensus structures during the alignment process, thus being able to achieve a high-quality alignment result. We apply BlockMatch to phylogeny reconstruction on a set of 5S rRNA sequences taken from fifteen bacteria species. Experimental results showed that the phylogenetic tree generated by our method is more accurate than the tree constructed based on the widely used ClustalW tool. The BlockMatch algorithm is implemented into a web server, accessible at http://bioinformatics.njit.edu/blockmatch. A jar file of the program is also available for download from the web server.
机译：我们提出了一种称为“ BlockMatch”的方法，用于比对两个模块，其中一个模块是具有斯德哥尔摩格式比对的共有二级结构的RNA多序列比对。该方法采用二次时间动态编程算法来对齐块中多个比对的列和列对。与许多其他只能对单个序列或结构进行成对比对的工具不同，BlockMatch在比对过程中考虑了块中所有序列的特征以及它们的共有结构，因此能够实现高质量的比对结果。我们将BlockMatch应用于从15种细菌中提取的一组5S rRNA序列的系统发育重建。实验结果表明，通过本方法生成的系统发育树比基于广泛使用的ClustalW工具构建的系统树更准确。 BlockMatch算法在Web服务器中实现，可从http://bioinformatics.njit.edu/blockmatch访问。也可以从Web服务器下载该程序的jar文件。

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