Poster abstracts
Poster number 125 submitted by Richard Watson
Recent Updates to the RNAstructure Software Package for RNA Secondary Structure Prediction and Analysis
Richard M. Watson (Biochemistry and Biophysics, University of Rochester), Michael Sloma (Biochemistry and Biophysics, University of Rochester), David H. Mathews (Biochemistry and Biophysics, University of Rochester)
Abstract:
RNAstructure is a suite of software tools for RNA secondary structure prediction, structure analysis, and sequence alignment. It is comprised of command-line programs, a desktop graphical user interface (GUI), and online webservers. RNAstructure has received a number of improvements over the past year. The programs can now predict structures for nucleic acids of any size alphabet, and therefore modified or designed residues can be included in structure prediction. The Java-based GUI has been enhanced with new tools and is now the primary GUI on all platforms (Windows, Mac OS X, and Linux). It now features a workflow-based UI in addition to the previous single-task operations. A new graphical structure editor has been added, which allows users to visually edit CT and dot-bracket structure files and also produce publication-quality RNA structure drawings.
Several new command-line tools have been added to the package: design generates a sequence to fold with low ensemble defect to a target structure. ProbScan calculates loop probabilities in thermodynamic ensembles. CycleFold predicts non-canonical base pairs. Rsample calculates basepair probabilities for a sequence that has multiple conformations. TurboFold II predicts alignments in addition to conserved RNA structures for a set of input RNA homologs.
Additional improvements have been made to quality control and distribution of the package; regression testing of the command-line tools has been enhanced and new regression tests of the GUI have been added. Improved installers are available for Windows and Mac operating systems. Parallel versions of most programs are now available to speed predictions on computers with multiple processor cores. Overall, these changes improve the ease, accuracy, and speed of RNA secondary structure analysis for users from a variety of backgrounds and skill levels.
References:
- Mathews, D.H., Turner, D.H., and Watson, R.M. 2016. RNA secondary structure prediction. Curr. Protoc. Nucleic Acid Chem. 67:11.2.1-11.2.19. doi: 10.1002/cpnc.19
- Spasic, A., Assmann, S.M., Bevilacqua, P.C. and Mathews, D.H. "Modeling RNA secondary structure folding ensemble using SHAPE mapping data." (Manuscript in preparation).
- Sloma, M.F. and Mathews, D.H. "Accurate prediction of RNA non-canonical pairs using probability estimates." (In review).
- Harmanci, A.O., Sharma, G., and Mathews, D.H. BMC Bioinformatics, 12:108. (2011).
- Reuter, J.S. and Mathews, D.H. "RNAstructure: software for RNA secondary structure prediction and analysis." BMC Bioinformatics, 11:129. (2010).
Keywords: RNA, Secondary Structure, Prediction