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R2R specifications

Information


Unique identifier OMICS_16669
Name R2R
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages C, C++, Perl
License GNU General Public License version 3.0
Computer skills Advanced
Version 1.0.4
Stability Stable
Maintained Yes

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  • person_outline Zasha Weinberg <>

Publication for R2R

R2R in publications

 (3)
PMCID: 4894983
PMID: 27229370
DOI: 10.1038/ncomms11667

[…] peak sequences with default parameters except for allowing a minimum single stem loop candidate length of 20 nt. the top-ranked motif incorporated 276 of the 328 sequences and was visualized by r2r., to check for overrepresentation of functional classes of csra-bound genes, we considered genes with at least fivefold enrichment in their 5′utr and/or coding sequence in the csra-3xflag coip […]

PMCID: 4509812
PMID: 26167874
DOI: 10.1038/nchembio.1846

[…] diagram. other rnas were predicted using rfam, trnascan-se, crt and rrna prediction. rho-independent transcription terminators were predicted using rnie. consensus diagrams were generated using r2r., as in a previous study, we collected genes located within 6 kilobases (kb) of a twister or hammerhead ribozyme where each gene is at least 200 base pairs from the end of a sequence fragment. […]

PMCID: 3111981
PMID: 21677862
DOI: 10.4056/sigs.1724282

[…] program currently takes inputs in fasta format, but will soon be modified to take stockholm format [] inputs for increased interoperability with other alignment software., zasha weinberg introduced r2r, software new application to aid in drawing publication-quality figures for single and consensus rna structures []. the goal of this software is to create structure drawing with both aesthetic […]

R2R institution(s)
Howard Hughes Medical Institute, Yale University, New Haven, CT, USA; Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT, USA; Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA

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