RME statistics

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Citations per year

Number of citations per year for the bioinformatics software tool RME

Tool usage distribution map

This map represents all the scientific publications referring to RME per scientific context
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RME specifications


Unique identifier OMICS_09336
Name RME
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages Perl, R
Computer skills Advanced
Stability Stable
Argparse, mixtools, reshape, MASS, evir, Bioconductor::preprocessCore
Maintained Yes


  • RNAstructure


No version available



  • person_outline Zhi John Lu

Publication for RME

RME citation


Modeling RNA secondary structure folding ensembles using SHAPE mapping data

Nucleic Acids Res
PMCID: 5758915
PMID: 29177466
DOI: 10.1093/nar/gkx1057

[…] ssible to an RNA because of thermal fluctuations. We also benchmarked Rsample for sequences that populate a single structure, and its performance was similar to other methods that can use SHAPE data: RME (), RNAprob (), RNAprobing (), RNAsc () and RNAstructure Fold (). […]

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RME institution(s)
MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, Center for Plant Biology and Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, China; Department of Computer Science and Engineering, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong, China; School of Biosciences, University of Exeter, UK Exeter, UK; Department of Biochemistry and Biophysics and Center for RNA Biology, University of Rochester Medical Center, Chinahester, NY, USA
RME funding source(s)
National Key Basic Research Program of China [2012CB316503]; National High-Tech Research and Development Program of China [2014AA021103]; National Natural Science Foundation of China [31271402]; Tsinghua University Initiative Scientific Research Program [2014z21045]; Hong Kong Research Grants Council Early Career Scheme [419612]; National Science Foundation [1339282]; Computing Platform of the National Protein Facilities (Tsinghua University)

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