GraphClust statistics

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Associated diseases

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GraphClust specifications

Information


Unique identifier OMICS_14803
Name GraphClust
Software type Pipeline/Workflow
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Maintained Yes

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Maintainer


  • person_outline Rolf Backofen <>

Publication for GraphClust

GraphClust in publications

 (4)
PMCID: 5882874
PMID: 29615754
DOI: 10.1038/s41598-018-23900-7

[…] of riboswitches., structural clustering of the tpp riboswitches was performed with multiple cluster threshold based on the infernal cmscore. the tools selected were rnascclust and its predecessor graphclust. graphclust input was the entire set of sequences while rnascclust received multiple sequence alignment for each of the three groups (bacteria, fungi, and oomycetes). in this analysis, […]

PMCID: 5712110
PMID: 29197323
DOI: 10.1186/s12864-017-4309-y

[…] from another viewpoint of image analysis, a few studies have been proposed where the distance is derived from a combination of histogram correlations and a geometrical distance measure [–]., graphclust [] clusters structured rna sequences based on hashing of the rna structures, followed by refinement of the clusters using structural alignment. rnasscclust [] extends graphclust to include […]

PMCID: 5068708
PMID: 27755571
DOI: 10.1371/journal.pone.0164726

[…] useful in topologically clustering rna families; however, rnashapes does not perform well on families with pseudoknots []. building on this work, heyne et al. developed a graph-based pipeline called graphclust [] for fast clustering of rna molecules. in this approach, rna secondary structures are generated by the rnashapes package from input sequences, encoded by graphs preserving nucleotide […]

PMCID: 4152356
PMID: 24755880
DOI: 10.4161/rna.28647

[…] used to classify all known crispr repeats. however, these alignment-based methods do not scale to efficiently cluster hundred of thousands of candidate ncrnas predicted by e.g. rnaz screens., with graphclust, a very different approach has become available. it avoids the alignment phase and the explicit computation of a distance matrix altogether. at the same time it is not restricted […]


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GraphClust institution(s)
Bioinformatics Group, Department of Computer Science, University of Freiburg, Freiburg, Germany
GraphClust funding source(s)
Supported by German Federal Ministry of Education and Research (BMBF) [0313921]; German Research Foundation [BA 2168/3-1 and BA 2168/4-1].

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