Professur für
Institute für Informatik
Universität Freiburg

GraphClust - structural clustering of local RNA secondary structures


GraphClust can be used for structural clustering of RNA sequences. Especially it can be used for clustering of very large dataset with thousands of RNAs. GraphClust was accepted and presented at ISMB 2012 in Long Beach, CA, USA.


With the GraphClust-0.7 release we incorporated CMfinder. Once a motif model is found from a dense center, we retrain the model. Usually this improves the model a lot!

0.7.6 bugfixes for Mac OSX and usage in SGE mode

0.7.5 bugfixes for Mac OSX, option for unstructured models

0.7.4 bugfixes

0.7.3 skip unstructured models

0.7.2 bugfixes

0.7.1 enables parallelization of NSPDK which speeds-up clustering stage 5; simply use '--threads ' (threads via openMP)


Latest Release: GraphClust-0.7.6 [zip] (July 2013)
Previous Release: GraphClust-0.7.5 [zip] (June 2013)


GraphClust runs on recent Linux systems. It is tested under Fedora 16 and Ubuntu 12.04. We have also a report that it runs under OSX 10.8. Thanks to JS!

GraphClust requires several tools to be installed:
LocARNA >= 1.7,
Vienna RNA Package >= 2.0
RNAz 2.1
Infernal 1.0.2 (1.1 is not supported yet!),
CMfinder 0.2 ,
RNAshapes 2.0.6,
and others.

Please see README file in source package for more information.

Using GraphClust

The README contains some basic information on how to use and configure GraphClust.


For any questions or issues concerning GraphClust please write an email to:
heyne [ @ ]