Computational approaches for RNA energy parameter estimation.

• If you use our algorithms or data in your work, we kindly ask you to cite the following publication:
  Computational approaches for RNA energy parameter estimation.
  Mirela Andronescu, Anne Condon, Holger Hoos, David Mathews and Kevin Murphy - RNA 16(12): 2304-2318, 2010.
  (see abstract and electronic version)
• Parameter estimation algorithms
  • Constraint Generation v2.0
  • Boltzmann Likelihood v2.0
• Secondary structure prediction algorithms
  • Simfold, part of MultiRNAFold v2.0 
• Parameter sets
  

  Parameter set	Model	MultiRNAFold format	Vienna RNA format	Mfold format
  BL-FR*	M7726	TXT -- BEST	--	--
  BL*	M363	TXT	TXT -- BEST	TAR.GZ -- BEST
  BL-no-dangles	M315	TXT	TXT	TAR.GZ
  NOM-CG	M363	TXT	TXT	TAR.GZ
  LAM-CG (CG*)	M363	TXT	TXT	TAR.GZ
  CG 1.1 (Andronescu 2007)	M363	TXT	TXT	TAR.GZ

• Download all the results, data sets, and scripts to generate predictions, tables and figures. [ DOWNLOAD ]
• The directory data contains all the data produced in this paper (parameter sets, stuctural and thermodynamic sets)
• The directory scripts contains programs and scripts to generate predictions, tables and figures shown in the paper.
• See the README file for details on how to run various scripts.
• The directory predictions contains predictions with various parameter sets, using scripts in the directory scripts.