RNA Folding on the 3D Triangular Lattice

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Delta A library that includes basic data structures and functions for the 3D triangular lattice, pull moves, file input/output, and RNA-specific information such as stacking pair energies. Application Programming Interface
Fold A folding simulation program for the prediction of RNA secondary structures and the reconstruction of RNA tertiary structures. Manual
Show A 3D visualization program for displaying the lattice conformations of RNA secondary structures and for playing RNA folding movies. Manual
Graphical User Interface
Select A program for selecting disjoint base pairs from the output of folding simulation. Manual
Convert A collection of conversion tools for different data formats. Data Formats
Documentation
Analyze Helper programs for the analysis of experimental results. Documentation
Make Traditional UNIX Makefiles for automating program compilation and experiments. Documentation

References

Joel Gillespie, Martin Mayne, and Minghui Jiang. RNA folding on the 3D triangular lattice. BMC Bioinformatics, 10:#369, 2009.
Minghui Jiang, Martin Mayne, and Joel Gillespie. Delta: a toolset for the structural analysis of biological sequences on a 3D triangular lattice. In Proceedings of the 2007 International Symposium on Bioinformatics Research and Applications (ISBRA'07), volume 4463 of Lecture Notes in Bioinformatics, pages 518-529, Springer-Verlag, 2007.
Joel Gillespie. Predicting RNA Secondary Structures by Folding Simulation: Software and Experiments. Master's thesis. Utah State University, 2009.
Martin Mayne. Folding Biological Sequences on a Three-Dimensional Triangular Lattice: Algorithms and Tools. Master's thesis. Utah State University, 2007.

Last modified: Thu Nov 5 13:53:27 MST 2009 _ _