GraphClust

GraphClust - Structural Clustering of Local RNA Secondary Structures

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GraphClust can be used for structural clustering of RNA sequences. It is particularly suited for clustering very large datasets with thousands of RNAs. GraphClust was accepted and presented at ISMB 2012 in Long Beach, CA, USA.

News

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• GraphClust-0.7: Incorporated CMfinder. Once a motif model is found from a dense center, we retrain the model for improved performance.
• Version 0.7.6: Bugfixes for macOS and SGE mode usage.
• Version 0.7.5: Bugfixes for macOS and option for unstructured models.
• Version 0.7.4: General bugfixes.
• Version 0.7.3: Skipping unstructured models.
• Version 0.7.2: General bugfixes.
• Version 0.7.1: Parallelization of NSPDK for faster clustering. Use --threads <NUM> for threading via OpenMP.

Download

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Latest Release

• GraphClust-0.7.6.tar.gz
• GraphClust-0.7.6.zip (July 2013)

Previous Release

• GraphClust-0.7.5.tar.gz
• GraphClust-0.7.5.zip (June 2013)

Installation

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GraphClust runs on recent Linux systems and has been tested under Fedora 16 and Ubuntu 12.04. It has also been reported to run on macOS 10.8 (thanks to JS!).

Requirements

GraphClust requires several tools to be installed:

• LocARNA >= 1.7
• Vienna RNA Package >= 2.0
• RNAz 2.1
• Infernal 1.0.2 (Note: version 1.1 is not supported yet!)
• CMfinder 0.2
• RNAshapes 2.0.6

For more information, refer to the README file in the source package.

Using GraphClust

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Refer to the README for basic information on how to use and configure GraphClust.

Problems/Questions?

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For any questions or issues concerning GraphClust, please write an email to: heyne [ @ ] informatik.uni-freiburg.de

Publication

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Steffen Heyne, Fabrizio Costa, Dominic Rose, and Rolf Backofen GraphClust: alignment-free structural clustering of local RNA secondary structures Bioinformatics, 2012, 28(12), i224-i232.