Package contextFold

The contextFold package supplies java source code for RNA secondary structure prediction utilities.

See:
          Description

Package contextFold Description

The contextFold package supplies java source code for RNA secondary structure prediction utilities. Its main uniqueness is in that it allows for a flexible scoring model design, and implements an efficient machine-learning algorithm for inferring weight parameters for such scoring models. Latest version is available at http://www.cs.bgu.ac.il/~negevcb/contextfold/.

The package is developed by Michal Ziv-Ukelson's bioinformatics group, Department of Computer Science, Ben Gurion University of the Negev, Israel. Group's homepage: http://www.cs.bgu.ac.il/~negevcb/. The main algorithmic notions are described in the papers:

[1] Shay Zakov, Yoav Goldberg, Michael Elhadad, and Michal Ziv-Ukelson. Rich Parameterization Improves RNA Structure Prediction. Research in Computational Molecular Biology (RECOMB 2011) 546-562.
[2] Koby Crammer, Ofer Dekel, Joseph Keshet, Shai Shalev-Shwartz, and Yoram Singer. Online Passive-Aggressive Algorithms. Journal of Machine Learning Research 7 (2006) 551–585.
[3] Rolf Backofen, Dekel Tsur, Shay Zakov, and Michal Ziv-Ukelson. Sparse RNA Folding: Time and Space Efficient Algorithms. Journal of Discrete Algorithms Volume 9, Issue 1, March 2011, Pages 12-31, 20th Anniversary Edition of the Annual Symposium on Combinatorial Pattern Matching (CPM 2009).

Copyright (C) 2010, 2011 Shay Zakov and Yoav Goldberg.

contextFold is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.

contextFold is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.

Contact:
Shay Zakov: zakovs@cs.bgu.ac.il
Yoav Goldberg: yoavg@cs.bgu.ac.il

Version:
1.00