PFold vs. RFAM-trained parameters
Below are bubbleplots of the covariant RNA basepair model from PFOLD, and similar models that were re-estimated using XRATE from various structure-annotated RNA alignment datasets:
|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.
- Knudsen & Hein: RNA secondary structure prediction using stochastic context-free grammars and evolutionary history. Bioinformatics 1999;15:446-54.
- Dowell & Eddy: Efficient pairwise RNA structure prediction and alignment using sequence alignment constraints. BMC Bioinformatics 2006;7:400.
- Xrate Software
- Bubble Plots
(For related discussion, see Rna Model Discussion)