Visualization tool for displaying an RNA structural ensemble. EnsembleRNA allows for comparison between structural ensembles for RNAs in different environments, as well as different variants of an RNA. SHAPE data can be incorporated into the ensemble prediction. Download the python package here.
Tool for identifying structure change in SHAPE data. This method classifies structure change into no change, local change and global change. The random forest model is built on a set of expert curated RNAs. Download the R package here.
Software that evaluates the effects of SNPs (Single Nucleotide Polymorphisms) on the ensemble structure of an RNA. It takes as input an RNA sequence and one or more SNPs, and then evaluates the structural consequences of the mutation by computing a WT/SNP correlation coefficient. The smaller the correlation the larger the structural effects of the SNP. The method is described in Halvorsen et al. 2010. Download the python package here.
A tool for predicting secondary structure of RNA using chemical and enzymatic mapping data. It is designed to take as input a combination of sequence and chemical probing data, and as output returns structures from the ensemble that are the closest match to the structural details contained within the probing data. The method is described in Martin & Quarrier et al. 2010.
The suite (downloadable here) is a series of Matlab scripts written in Mathwork’s Matlab software package. This collection of programs is designed to read in the output from the Beckman sequencer, and then align, scale and assemble files for use with ShapeFinder (created in the Giddings Lab at the University of North Carolina at Chapel hill). Justin Ritz has created a tutorial on the use of this software as well as the use of the output in ShapeFinder. The movies can be found on YouTube and here: CEQ Tutorial, ShapeFinder Tutorial Part 1, Part 2, and Part 3.
A standard for reporting Single Nucleotide Resolution Nucleic Acid Structure Mapping data in a consistent and machine readable way.
(Semi-Automated Footprinting Analysis) is software to analyze and quantify footprinting gels in a fast and accurate way.
(Capillary Automated Footprinting Analysis) allows for the analysis and quantification of chemical mapping experiments carried out in a capillary sequencer.
Software for modeling RNA folding experiments (time-resolved) using hydroxyl radical footprinting data.
(Nucleic Acid Simulation Tool) is a a coarse-grained molecular modeling package for 3D RNA structure prediction and analysis.