Finding the most significant common sequence and structure motifs in a set of RNA sequences
Finding the most significant common sequence and structure motifs in a set of RNA sequences
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DOI：
10.1093/nar/25.18.3724
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发表时间：
1997-09-15
影响因子：
14.9
通讯作者：
Stormo, GD
中科院分区：
文献类型：
--
作者：
Gorodkin, J;Heyer, LJ;Stormo, GD
我们提出了一种利用序列和结构约束对RNA序列进行局部比对的计算方法。此外，该方法在所有可能的序列中搜索具有最重要的共同基序的比对结果。第一部分利用简化的Sankoff算法同时进行RNA序列的折叠和比对，但是通过从成对比较构建多序列比对来保持易处理性。该算法使用贪婪方法找到多序列比对并且与CLUSTAL和CONSENSUS两者具有相似性，但是核心算法确保成对比对对于序列和结构保守性都是最优化的。评分系统的选择和逐步构建最终解决方案的方法是重要的考虑因素，讨论，示例解决方案，并与其他方法的比较，提供的解决方案，包括寻找一致的结构相同的出版的。
We present a computational scheme to locally align a collection of RNA sequences using sequence and structure constraints, In addition, the method searches for the resulting alignments with the most significant common motifs, among all possible collections, The first part utilizes a simplified version of the Sankoff algorithm for simultaneous folding and alignment of RNA sequences, but maintains tractability by constructing multi-sequence alignments from pairwise comparisons, The algorithm finds the multiple alignments using a greedy approach and has similarities to both CLUSTAL and CONSENSUS, but the core algorithm assures that the pairwise alignments are optimized for both sequence and structure conservation. The choice of scoring system and the method of progressively constructing the final solution are important considerations that are discussed, Example solutions, and comparisons with other approaches, are provided, The solutions include finding consensus structures identical to published ones.