RNAscClust specifications


Unique identifier OMICS_16457
Name RNAscClust
Software type Pipeline/Workflow
Interface Command line interface
Restrictions to use None
Input data A set of multiple structural alignments of RNA sequences.
Output data The secondary structure for the sequence from the organism of interest in each alignment, the candidate clusters.
Operating system Unix/Linux
License GNU General Public License version 3.0
Computer skills Advanced
Version 1.0.0
Stability Stable
Source code URL http://www.bioinf.uni-freiburg.de/Software/RNAscClust/Releases/RNAscClust-1.0.0.tar.gz
Maintained Yes


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  • person_outline Rolf Backofen <>

Publication for RNAscClust


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

2017 Bioinformatics
PMCID: 5870858
PMID: 28334186
DOI: 10.1093/bioinformatics/btx114
Milad Miladi
Milad Miladi
Milad Miladi
Milad Miladi
Milad Miladi
Milad Miladi
Milad Miladi
Milad Miladi

RNAscClust in publications

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

[…] generate the secondary structure 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, […]

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

[…] 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 high […]

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RNAscClust funding source(s)
This work was supported by Innovation Fund Denmark, the Danish Center for Scientific Computing (DCSC/DeiC), the Danish Cancer Society and by the Deutsche Forschungsgemeinschaft (DFG, MO 2402/1- 1, BA 2168/4-2, BA 2168/3-3 A).

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