RNAscClust: clustering RNA sequences using structure conservation and graph based motifs
RNAscClust: clustering RNA sequences using structure conservation and graph based motifs
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DOI：
10.1093/bioinformatics/btx114
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发表时间：
2017-07-15
期刊：
影响因子：
5.8
通讯作者：
Backofen, Rolf
中科院分区：
文献类型：
--
作者：
Miladi, Milad;Junge, Alexander;Backofen, Rolf
动机：将具有共同二级结构的RNA序列聚类是研究RNA功能的重要一步。尽管结构RNA比对策略通常识别直向结构RNA的共同结构，但聚类试图基于结构相似性对旁系同源RNA进行分组。然而，现有的方法用于聚类旁系同源RNA，不考虑补偿性的碱基对的变化，从结构保守的orthopathic sequences.Results：在这里，我们提出了RNAscClust，一个新的算法来聚类一组结构化的RNA，考虑到它们各自的结构保守的实施。对于一组RNA序列的多重结构比对，每个序列都包含一个包含在其直系同源物结构比对中的同源序列，RNAscClust使用保守碱基对作为折叠的先验信息计算每个序列的最小自由能结构。然后使用基于图核的策略对旁系同源物进行聚类，该策略识别共同的结构特征。我们表明，聚类精度明显受益于补偿性碱基对变化的比对程度的增加。
Motivation: Clustering RNA sequences with common secondary structure is an essential step towards studying RNA function. Whereas structural RNA alignment strategies typically identify common structure for orthologous structured RNAs, clustering seeks to group paralogous RNAs based on structural similarities. However, existing approaches for clustering paralogous RNAs, do not take the compensatory base pair changes obtained from structure conservation in orthologous sequences into account.Results: Here, we present RNAscClust, the implementation of a new algorithm to cluster a set of structured RNAs taking their respective structural conservation into account. For a set of multiple structural alignments of RNA sequences, each containing a paralog sequence included in a structural alignment of its orthologs, RNAscClust computes minimum free-energy structures for each sequence using conserved base pairs as prior information for the folding. The paralogs are then clustered using a graph kernel-based strategy, which identifies common structural features. We show that the clustering accuracy clearly benefits from an increasing degree of compensatory base pair changes in the alignments.