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Efficient RNA structure comparison algorithms

机译：高效的RNA结构比较算法

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摘要

Recently proposed relative addressing-based (rab) RNA secondary structure representation has important features by which an RNA structure database can be stored into a suffix array. A fast substructure search algorithm has been proposed based on binary search on this suffix array. Using this substructure search algorithm, we present a fast algorithm that finds the largest common substructure of given multiple RNA structures in rab format. The multiple RNA structure comparison problem is NP-hard in its general formulation. We introduced a new problem for comparing multiple RNA structures. This problem has more strict similarity definition and objective, and we propose an algorithm that solves this problem efficiently. We also develop another comparison algorithm that iteratively calls this algorithm to locate nonover-lapping large common substructures in compared RNAs. With the new resulting tools, we improved the RNASSAC website (linked from http://faculty.tamuc.edu/aarslan). This website now also includes two drawing tools: one specialized for preparing RNA substructures that can be used as input by the search tool, and another one for automatically drawing the entire RNA structure from a given structure sequence.
机译：最近提出的基于相对寻址（RAB）RNA二级结构表示具有重要特征，通过该特征可以将RNA结构数据库存储到后缀阵列中。已经基于该后缀阵列的二进制搜索提出了一种快速的子结构搜索算法。使用该子结构搜索算法，我们提出了一种快速算法，该算法在RAB格式中找到给定多个RNA结构的最大常见副结构。多RNA结构比较问题在其一般配方中是NP - 硬。我们介绍了比较多个RNA结构的新问题。这个问题具有更严格的相似性定义和目标，我们提出了一种算法，可以有效解决这个问题。我们还开发了另一种比较算法，其迭代地称该算法呼叫该算法以定位比较RNA中的非传播大的常见子结构。通过新的结果工具，我们改进了Rnassac网站（从http://faculty.tamuc.edu/aarslan相关联）。本网站现在还包括两个绘图工具：专门用于准备可以用作搜索工具的输入的RNA子结构，另一个用于从给定结构序列自动绘制整个RNA结构的RNA子结构。

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