RNAmotifs statistics

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Associated diseases

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RNAmotifs specifications


Unique identifier OMICS_02287
Name RNAmotifs
Software type Application/Script
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages Python
License MIT License
Computer skills Advanced
Version 2.0.1
Stability Stable
Maintained Yes



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  • person_outline Jernej Ule <>
  • person_outline Gregor Rot <>

Publication for RNAmotifs

RNAmotifs in publications

PMCID: 4808798
PMID: 26751491
DOI: 10.3390/biom6010004

[…] peak calling algorithm for par-clip datasets only. finally, motif recognition algorithms are used to identify motifs recognized by rbp. algorithms such as memeris, phylogibbs, rnacontext, and rnamotifs identify motifs at the rna level, while meme, cermit, glam2, and matrixreduce were developed to identify motif at the dna level. lastly, the identified rbp motif is analyzed using mcarts […]

PMCID: 4689037
PMID: 26694817
DOI: 10.1186/s12915-015-0220-7

[…] association of safb1 with splicing we used exon array analysis and found safb1 knockdown mediated the statistically significant up- and downregulation of alternative exons. further analysis using rnamotifs to investigate the frequency of association between the motif pairs (aga followed by aga, gaa or aag) and alternative spliced exons found there was a highly significant correlation […]

PMCID: 4653638
PMID: 26586468
DOI: 10.1038/srep17059

[…] in either utr of the 213 mrnas that had longer tails in the kos. however, there was no enrichment of any specific rna sequence found by homer rna motif analysis (http://homer.salk.edu/homer/motif/rnamotifs.html) (data not shown), although this does not rule out the possibility that noc recognizes a cis motif defined by rna secondary structure, rather than rna sequence., […]

PMCID: 3919595
PMID: 24217913
DOI: 10.1093/nar/gkt1118

[…] nt. sequence interval numbering is with respect to the translational start site (atg)., for prediction of rna structures, we used the ‘segal tool’ rnapromo (http://genie.weizmann.ac.il/pubs/rnamotifs08/rnamotifs08_predict.html). this tool predicts a structural motif common to a set of given rna sequences. the folding algorithm used in the segal method is the ‘vienna package’ […]

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RNAmotifs institution(s)
Institute of Molecular Life Sciences and Swiss Institute of Bioinformatics, Zurich, Switzerland; MRC Laboratory of Molecular Biology, Cambridge, UK; Institut de Biologie de l’ENS (IBENS), Paris, France; UCL Institute of Neurology, Queen Square, London, UK; The Francis Crick Institute, London, UK; European Molecular Biology Laboratory, Heidelberg, Germany; Institute of Stem Cell Research, Helmholtz Center Munich, Neuherberg, Germany; Institute of Molecular Biology, Mainz, Germany; Faculty of Computer and Information Science, University of Ljubljana, Ljubljana, Slovenia
RNAmotifs funding source(s)
Supported by the European Research Council (206726-CLIP and 617837-Translate) and the Slovenian Research Agency (J7-5460); and by the Swiss National Science Foundation (grant 31003A_160095).

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