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RNACluster: An integrated tool for RNA secondary structure comparison and clustering
Author(s) -
Liu Qi,
Olman V.,
Liu Huiqing,
Ye Xiuzi,
Qiu Shilun,
Xu Ying
Publication year - 2008
Publication title -
journal of computational chemistry
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.907
H-Index - 188
eISSN - 1096-987X
pISSN - 0192-8651
DOI - 10.1002/jcc.20911
Subject(s) - rna , cluster analysis , nucleic acid secondary structure , representation (politics) , identification (biology) , computer science , cluster (spacecraft) , protein secondary structure , computational biology , nucleic acid structure , hierarchical clustering , data mining , theoretical computer science , biological system , chemistry , biology , artificial intelligence , biochemistry , botany , politics , political science , law , gene , programming language
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. © 2008 Wiley Periodicals, Inc. J Comput Chem, 2008