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Rtools specifications


Unique identifier OMICS_11651
Name Rtools
Interface Web user interface
Restrictions to use None
Input data Single RNA sequence <= 400nt
Input format FASTA
Output data Rtools returns various analyses based on secondary structures for the sequence.
Output format TEXT, PNG, PDF and EPS
Computer skills Basic
Stability Stable
Maintained Yes


  • person_outline Kiyoshi Asai

Publication for Rtools

Rtools citations


Effects of mRNA secondary structure on the expression of HEV ORF2 proteins in Escherichia coli

Microb Cell Fact
PMCID: 5686824
PMID: 29137642
DOI: 10.1186/s12934-017-0812-8

[…] gene, the secondary structure of the mRNA (− 43/AUG/+ 43) sequence containing the ribosome-binding site (RBS), translation initiator AUG and the first 14 codons, was predicted and analyzed using the Rtools web server (http://rtools.cbrc.jp/cgi-bin/index.cgi). This server provides a rich set of tools for analyzing a single RNA sequence:We used the CentroidFold tool for the structure prediction []. […]


Revealing Neurocomputational Mechanisms of Reinforcement Learning and Decision Making With the hBayesDM Package

PMCID: 5869013
PMID: 29601060
DOI: 10.1162/CPSY_a_00002

[…] an can be installed just by entering the following command into the R console: install.packages("rstan", dependencies=TRUE) For Windows, it is necessary to install Rtools before installing RStan. Instructions for installing Rtools on a Windows machine can be found at this link (https://github.com/stan-dev/rstan/wiki/Install-Rtools-for-Windows). After RStan (as w […]


A pilot study demonstrating the altered gut microbiota functionality in stable adults with Cystic Fibrosis

Sci Rep
PMCID: 5532234
PMID: 28751714
DOI: 10.1038/s41598-017-06880-y

[…] gnificant result (all values have been corrected for multiple testing with the benjamini-hochberg method). Principle coordinate analysis (PCA) and heat maps were generated using the ggplots2, gplots, Rtools, devtools and cluster packages in R. The 3D scatter plots were generated with the following axes: on the x-axis carbohydrate metabolic process = GO:0005975|BP|03|, lipid metabolic process on th […]


Computational prediction of lncRNA mRNA interactionsby integrating tissue specificity in human transcriptome

Biol Direct
PMCID: 5465533
PMID: 28595592
DOI: 10.1186/s13062-017-0183-4

[…] all the human genes were obtained from the Expression Atlas (accession numbers are listed in Additional file 10). All sequence-based predictions of lncRNA-mRNA interactions were obtained from http://rtools.cbrc.jp/cgi-bin/RNARNA/index.pl. […]


Testing Separability and Independence of Perceptual Dimensions with General Recognition Theory: A Tutorial and New R Package (grtools)

Front Psychol
PMCID: 5440596
PMID: 28588513
DOI: 10.3389/fpsyg.2017.00696

[…] The grtools package uses the computer programming language R (). R is an open-source statistical software used by many researchers across a variety of scientific fields. R can be downloaded for free at htt […]


Characterization of long noncoding RNA and messenger RNA signatures in melanoma tumorigenesis and metastasis

PLoS One
PMCID: 5321451
PMID: 28225791
DOI: 10.1371/journal.pone.0172498

[…] using the Cytoscape 3.4.0 program. The degree was defined as the number of directly linked neighbors. We further validated lncRNA-mRNA interactions in a database developed by Terai et al. [] (http://rtools.cbrc.jp/cgi-bin/RNARNA/index.pl), which included all the predicted RNA-RNA interactions using 23,898 lncRNA and 81,814 mRNA sequences obtained from the Gencode project (http://www.gencodegenes. […]


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Rtools institution(s)
Department of Electrical Engineering and Bioscience, Faculty of Science and Engineering, Waseda University, Tokyo, Japan; Artificial Intelligence Research Center (AIRC), National Institute of Advanced Industrial Science and Technology (AIST), Tokyo, Japan; IMSBIO Co., Ltd, Tokyo, Japan; Graduate School of Frontier Sciences, University of Tokyo, Japan; Department of Biosciences and Informatics, Keio University, Yokohama, Japan; Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto, Japan
Rtools funding source(s)
MEXT KAKENHI (Grant-in-Aid for Young Scientists (A) [24680031, in part]; Grant-in- Aid for Scientific Research (A) [25240044]; Grant-in-Aid for Scientific Research on Innovative Areas [221S0002]

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