title: RNACluster: An integrated tool for RNA secondary structure comparison and clustering.
abstract: RNA structure comparison is a fundamental problem in structural biology, structural chemistry, and bioinformatics. It can be used for analysis of RNA energy landscapes, conformational switches, and facilitating RNA structure prediction. The purpose of our integrated tool RNACluster is twofold: to provide a platform for computing and comparison of different distances between RNA secondary structures, and to perform cluster identification to derive useful information of RNA structure ensembles, using a minimum spanning tree (MST) based clustering algorithm. RNACluster employs a cluster identification approach based on a MST representation of the RNA ensemble data and currently supports six distance measures between RNA secondary structures. RNACluster provides a user-friendly graphical interface to allow a user to compare different structural distances, analyze the structure ensembles, and visualize predicted structural clusters.
authors.affiliation: James D. Watson Institute of Genomic Science, Zhejiang University, Hangzhou 310008, China.
authors.forename: Qi
authors.initials: Q
authors.lastname: Liu
authors.forename: V
authors.initials: V
authors.lastname: Olman
authors.forename: Huiqing
authors.initials: H
authors.lastname: Liu
authors.forename: Xiuzi
authors.initials: X
authors.lastname: Ye
authors.forename: Shilun
authors.initials: S
authors.lastname: Qiu
authors.forename: Ying
authors.initials: Y
authors.lastname: Xu
mesh_terms: D000465:Algorithms; D016000:Cluster Analysis; D003198:Computer Simulation; D009690:Nucleic Acid Conformation; D009711:Nucleotides / Q000737:chemistry; D011237:Predictive Value of Tests; D012313:RNA / Q000737:chemistry*; D012984:Software
chemical_list: D009711:Nucleotides; D012313:RNA