Rtools protocols

View Rtools computational protocol

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Rtools specifications

Information


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

Maintainer


  • person_outline Kiyoshi Asai <>

Publication for Rtools

Rtools in pipeline

2017
PMCID: 5465533
PMID: 28595592
DOI: 10.1186/s13062-017-0183-4

[…] [], tantan [], last [, ], intarna [], and ractip [], for predicting human lncrna-rna interactions []. furthermore, all predicted human lncrna-rna interactions are available from our database (http://rtools.cbrc.jp/cgi-bin/rnarna/index.pl). our database contains the lncrna-mrna and lncrna-lncrna interactions between 23,898 lncrnas and 20,185 mrna sequences obtained from the gencode project […]


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Rtools in publications

 (10)
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 […]

PMCID: 5869013
PMID: 29601060
DOI: 10.1162/CPSY_a_00002

[…] 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 […]

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

[…] 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 […]

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

[…] [], tantan [], last [, ], intarna [], and ractip [], for predicting human lncrna-rna interactions []. furthermore, all predicted human lncrna-rna interactions are available from our database (http://rtools.cbrc.jp/cgi-bin/rnarna/index.pl). our database contains the lncrna-mrna and lncrna-lncrna interactions between 23,898 lncrnas and 20,185 mrna sequences obtained from the gencode project […]

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 […]


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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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