RME statistics

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Citations per year

Number of citations per year for the bioinformatics software tool RME
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Tool usage distribution map

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

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RME specifications

Information


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
Requirements
Argparse, mixtools, reshape, MASS, evir, Bioconductor::preprocessCore
Maintained Yes

Subtool


  • RNAstructure

Versioning


No version available

Documentation


Maintainer


  • person_outline Zhi John Lu

Publication for RME

RME citation

library_books

Modeling RNA secondary structure folding ensembles using SHAPE mapping data

2017
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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