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首页> 外文会议>International Conference on String Processing and Information Retrieval(SPIRE 2004); 20041005-08; Padova(IT) >Fast Detection of Common Sequence Structure Patterns in RNAs
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Fast Detection of Common Sequence Structure Patterns in RNAs

机译：RNA中常见序列结构模式的快速检测

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摘要

We developed a dynamic programming approach of computing common sequence/structure patterns between two RNAs given by their sequence and secondary structures. Common patterns between two RNAs are meant to share the same local sequential and structural properties. Nucleotides which are part of an RNA are linked together due to their phosphodiester or hydrogen bonds. These bonds describe the way how nucleotides are involved in patterns and thus delivers a bond-preserving matching definition. Based on this definition, we are able to compute all patterns between two RNAs in time O(nm) and space O(nm), where n and m are the lengths of the RNAs, respectively. Our method is useful for describing and detecting local motifs and for detecting local regions of large RNAs although they do not share global similarities. An implementation is available in C++ and can be obtained by contacting one of the authors.
机译：我们开发了一种动态编程方法，可以计算两个RNA之间由其序列和二级结构给定的通用序列/结构模式。两个RNA之间的共有模式旨在共享相同的局部顺序和结构特性。作为RNA一部分的核苷酸由于其磷酸二酯或氢键而连接在一起。这些键描述了核苷酸如何参与模式的方式，从而提供了一个保留键的匹配定义。基于此定义，我们能够计算两个RNA在时间O（nm）和空间O（nm）之间的所有模式，其中n和m分别是RNA的长度。尽管它们不具有全局相似性，但我们的方法可用于描述和检测局部基序以及检测大RNA的局部区域。 C ++中提供了一个实现，可以通过与一位作者联系获得该实现。

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