PFold vs. RFAM-trained parameters

Original Pfold parameters	RFAM-trained parameters	rRNA-trained parameters

The rRNA-trained parameters (right) were estimated from the CONSAN mix80 dataset, derived by Dowell & Eddy from the European rRNA database.

References:

• Knudsen B, Hein J.  RNA secondary structure prediction using stochastic context-free grammars and evolutionary history.  Bioinformatics. 1999 Jun;15(6):446-54.
• Dowell RD, Eddy SR.  Efficient pairwise RNA structure prediction and alignment using sequence alignment constraints.  BMC Bioinformatics. 2006 Sep 4;7:400.
• Xrate Software
• Bubble Plots

(For related discussion, see Rna Model Discussion)