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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


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  • person_outline Zhi John Lu <>

Publication for RME

RME in publications

PMCID: 5907308
DOI: 10.1186/s13098-018-0315-8

[…] that is the nih genetic sequence database. the sequences obtained were aligned with the clustal w multiple alignment algorithms. for the molecular modeling, the structures were generated with the rnastructure, a fully automated mirnas structure modelling server, accessible via the web servers for rna secondary structure prediction., results: we demonstrated a search for nucleotide sequence […]

PMCID: 5933463
PMID: 29708552
DOI: 10.3791/57379

[…] and under a license granted to d. becquet (préfecture des bouches-du-rhône, authorization no. 13-002)., using the primary sequence of the lncrna of interest, generate its secondary structure on the "rnastructure webserver". note: on this site, different algorithms can be used. the three prediction tools that give the best results for the probe designs are: "fold" (lowest free energy structure), […]

PMCID: 5882922
PMID: 29615727
DOI: 10.1038/s41598-018-23845-x

[…] 4 and 5 require long timescales to achieve their final conformation., to gain information about the ires conformational changes induced by the interaction with r fraction we took advantage of the rnastructure software incorporating the shape reactivity data, and the rnacomposer server. the predicted structure of the free ires element treated with ia is depicted in fig. . upon incubation […]

PMCID: 5886760
PMID: 29409859
DOI: 10.1016/j.molp.2018.01.008

[…] energy function (). their cds were folded as well. the phylogenetic structure of 18s rrna was downloaded from the comparative rna web site (http://www.rna.icmb.utexas.edu/). the scorer utility in rnastructure (rnastructure-5.8.1) was used for ppv and sensitivity calculation. the f1 score was calculated from the previous definition (). when comparing ppv in cds between rice and arabidopsis, […]

PMCID: 5853050
PMID: 29540207
DOI: 10.1186/s12977-018-0407-4

[…] described previously []. outliers were defined as above and were removed from the dataset. these constituted less than 8% of values. the average reactivities were then used as shape constraints in rnastructure [] to predict structural models and their free energies., nsc was previously observed to prevent gag interacting with sl3 in vitro and to stabilize the rna. structural rearrangement […]

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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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