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RNACluster - An intergrated tool for RNA secondary structure comparison and clustering

 

 
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Overview

RNACluster is an integrated computational software which implements 6 common structure distances to measure the (dis)similarity of RNA secondary structures including base pair distance, mountain distance, morphological distance, tree edit distance, string edit distance and our in-house structure matrix distance, and one effective cluster approach for the ensemble clustering using a minimum spanning tree (MST) based algorithm. RNACluster can be used to study the characteristics of RNA secondary structures, RNA structure conformational switches, RNA conformational energy landscapes and RNA secondary structure prediction based on the clustering of structure ensemble.

RNACluster was written in C++ and matlab,compiled in Windows and Linux, and run on both platforms. We have supplied three versions of RNACluster:Windows console version; Windows graphic version and Linux version.

The output of RNACluster will be the distance matrix of a given structure ensemble and the clustering result of the ensemble based on Minimum Spanning Tree(MST) algorithm. Format of distance matrix is followed with the format of input to the programs fitch, kitsch and neighbor in PHYLIP package, which can be used to construct the hierarchical or phylogeny tree of the input RNA structure samples.


Download

  • RNACluster 1.0 , Windows console version without graphic interface. Download
  • RNACluster 1.0 , Windows graphic version. Download
  • RNACluster 1.0 , Linux version. Download

Documentation

  • To download the documentation for RNACluster 1.0 as PDF file click here
  • To download the documentation for RNACluster 1.0 as Microsoft Word file click here

Supplementary materials

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Reference

Qi Liu, V. Olman, Huiqing Liu, Xiuzi Ye,Shilun Qiu,Ying Xu. RNACluster: An integrated tool for RNA structures comparison and clustering, To be submitted to the Journal of Computational Chemistry.

Ying Xu, V. Olman, Dong Xu. Clustering gene expression data using a graph-theoretic approach:an application of minimum spanning trees,Bioinformatics,Vol.18,No.4(2002),536-545.click here

V. Olman, Dong Xu, Ying Xu. CUBIC: Identification of regulatory binding sites through data clustering,Journal of Bioinformatics and Computational Biology,Vol.1,No.1(2003),21-40.click here


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Contact

Email: qiliu@csbl.bmb.uga.edu

Qi Liu

Last updated 10/01/2007