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Citations per year

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CapR specifications


Unique identifier OMICS_09337
Name CapR
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages C++
Computer skills Advanced
Stability Stable
Maintained Yes




No version available


  • person_outline Tsukasa Fukunaga

Publication for CapR

CapR 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

[…] ecognizing specific RNA sequences presented in specific structures. Therefore, we investigated the exposition of the SD sequence and the start codon using two different algorithms. First, we used the CapR algorithm to calculate the probabilities for each RNA base position to be within one of six different secondary structural contexts. The results showed that in the mRNA of the non-expressed genes […]


Integrating Epigenomics into the Understanding of Biomedical Insight

Bioinform Biol Insights
PMCID: 5138066
PMID: 27980397
DOI: 10.4137/BBI.S38427

[…] ormed well, which include HOMER, MEME, cERMIT, GLAM2, MatrixREDUCE, and RNAcontext. Although there are tools for the ncRNA secondary structure prediction and functional annotation, such as GraphProt, CapR, and LncRNA2Function, there are still significant challenges in this field including increasing the sensitivity and specificity, decreasing the false-positive discovery rate, and expanding the al […]


Design and bioinformatics analysis of genome wide CLIP experiments

Nucleic Acids Res
PMCID: 4477666
PMID: 25958398
DOI: 10.1093/nar/gkv439

[…] d RNAs, so intramolecular structures formed by the double-strand part of RNAs could actually inhibit RBP binding (). Many tools have been developed to predict the secondary structures of RNA, such as CapR (), RNAcontext () and RNAfold (). […]

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CapR institution(s)
Department of Computational Biology, Graduate School of Frontier Sciences, the University of Tokyo, Chiba, Japan; INTEC Inc, Tokyo, Japan; Computational Biology Research Center, National Institute of Advanced Industrial Science and Technology, Tokyo, Japan; Atmosphere and Ocean Research Institute, University of Tokyo, Chiba, Japan
CapR funding source(s)
This study was supported by JSPS KAKENHI Grant Numbers 22240031, 23710231, 25134701 and 25870190.

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