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RNAscClust: Clustering RNA Sequences Using Structure Conservation and Graph Based Motifs

Milad MiladiAlexander JungeFabrizio CostaStefan E SeemannJakob Hull HavgaardJan GorodkinRolf Backofen

出版	Universität, 2017
URL	http://books.google.com.hk/books?id=OE2zzwEACAAJ&hl=&source=gbs_api

註釋Abstract: 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.

Availability and Implementation
RNAscClust is available at http://www.bioinf.uni-freiburg.de/Software/RNAscClust