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Number of citations per year for the bioinformatics software tool GraphClust
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Protocols

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

Versioning


No version available

Maintainer


  • person_outline Rolf Backofen

Publication for GraphClust

GraphClust citations

 (7)
library_books

Phylogenomic and comparative analysis of the distribution and regulatory patterns of TPP riboswitches in fungi

2018
Sci Rep
PMCID: 5882874
PMID: 29615754
DOI: 10.1038/s41598-018-23900-7

[…] 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, the […]

call_split

DotAligner: identification and clustering of RNA structure motifs

2017
Genome Biol
PMCID: 5747123
PMID: 29284541
DOI: 10.1186/s13059-017-1371-3
call_split See protocol

[…] t’ object without transformation, and subjected to OPTICS clustering as implemented in the dbscan CRAN repository with a range of parameters (see Fig.  , ).Other tested RNA clustering approaches were GraphClust and NoFold. We ran GraphClust version 0.7.6 inside the Docker image provided with RNAscClust with default parameters. NoFold version 1.0.1 uses 1973 Rfam CMs by default as empirical feature […]

library_books

Alignment free comparative genomic screen for structured RNAs using coarse grained secondary structure dot plots

2017
BMC Genomics
PMCID: 5712110
PMID: 29197323
DOI: 10.1186/s12864-017-4309-y

[…] h sensitivity using the output of the current scan as input;Then use a structural alignment method optimized for finding local structural alignments like Foldalign [];Finally cluster the results with GraphClust [] or RNAscClust [] to find families of structures. A method like Structator [] could be used to search for missed members of the clusters. Rerun DotcodeR with a step size of 10 and a very […]

call_split

RNAscClust: clustering RNA sequences using structure conservation and graph based motifs

2017
Bioinformatics
PMCID: 5870858
PMID: 28334186
DOI: 10.1093/bioinformatics/btx114
call_split See protocol

[…] By design, each subalignment in the Rfam-ome and Rfam-cliques benchmarks contains a human sequence. This enables the comparison of RNAscClust and GraphClust by measuring the degree to which Rfam families are reconstructed using human sequences alone and comparing the outcome to an RNAscClust result harnessing covariance information contained in […]

library_books

Accurate Classification of RNA Structures Using Topological Fingerprints

2016
PLoS One
PMCID: 5068708
PMID: 27755571
DOI: 10.1371/journal.pone.0164726

[…] re the similarity of RNA secondary structures represented by dual graphs [, ]; Liu et al. developed a fuzzy kernel to cluster the secondary structure ensemble generated from a single sequence []. The GraphClust pipeline developed by Heyne et al. encodes RNA sequence-structure information as graphs and measures RNA graph similarities using a decomposition kernel and computing the summed similarity […]

library_books

phylosignal: an R package to measure, test, and explore the phylogenetic signal

2016
Ecol Evol
PMCID: 4799788
PMID: 27066252
DOI: 10.1002/ece3.2051

[…] tests for each bootstrap. The function renders the results as boxplots allowing assessing the effect of phylogenetic reconstruction uncertainty on phylogenetic signal estimates. Finally, the function graphClust implements a simple method to perform traits clustering under phylogenetic constraints (Keck et al. ). […]


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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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