RNAshapes 3.3.0 – RNA Analysis Package based on Abstract Shapes

RNAshapes 3.3.0

:: DESCRIPTION

RNAshapes  abstraction maps structures to a tree-like domain of shapes, retaining adjacency and nesting of structural features, but disregarding helix lengths. Shape abstraction integrates well with dynamic programming algorithms, and hence it can be applied during structure prediction rather than afterwards. This avoids exponential explosion and can still give us a non-heuristic and complete account of properties of the molecule’s folding space.

::DEVELOPER

Stefan Janssen

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

RNAshapes

:: MORE INFORMATION

Citation

The RNA shapes studio.
Janssen S, Giegerich R.
Bioinformatics. 2015 Feb 1;31(3):423-5. doi: 10.1093/bioinformatics/btu649.

P. Steffen, B. Voß, M. Rehmsmeier, J. Reeder, and R. Giegerich.
RNAshapes: an integrated RNA analysis package based on abstract shapes
Bioinformatics, 22(4), 2006.

RnallViewer 1.0.1 – RNA Analysis Visualization Tool

RnallViewer 1.0.1

:: DESCRIPTION

RnallViewer is an RNA analysis and visualization tool that combines information and processing from various command-line tools in an intuitive graphical user interface (GUI). Rnall is used for generating RNA structure predictions, which can be automatically sent to Naview, plt22ps, and Ghostscript for visualization. Annotation information can be included, parsed with the help of BioJava. RnallViewer’s panelling system allows much of this information to be displayed simultaneously, and comprehensive searching methods allow quick access to specific regions based on annotation and position criteria in the format of NCBI ptt format

::DEVELOPER

Systems Biology Laboratory, College of Veterinary Medicine,Mississippi State University

:: SCREENSHOTS

:: REQUIREMENTS

:: DOWNLOAD

RnallViewer

:: MORE INFORMATION

Citation

Wan, X.-F., P. P. Dempsey, and D. Xu. 2008.
RnallViewer: A tool for RNA local secondary structure prediction, localization, and visualization.
International Journal of Computational Science, Special Issue on Bioinformatics and Computational Biology, 2(5): 607-612.