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