Integrating Chemical Footprinting Data into RNA
Secondary Structure Prediction
http://www.ncbi.nlm.nih.gov/pmc/artic…
Source code & Web server
http://bioinformatics.bc.edu/clotelab…
Also this:
RNA folding with soft constraints: reconciliation
of probing data and thermodynamic secondary structure prediction
About the first link you posted, if I understand correctly :
Sequence -> Predictor (here, Vienna 1.8x) -> the MFE structure we know so well (natural mode)
Sequence + SHAPE raw data -> Predictor (RNAsc) -> a very precise prediction of how it actually folded
This would be an apparently perfect replacement for the estimation mode when viewing lab results.
And this one is even better, because it’s a fork of ViennaRNA, meaning that the development team at EteRNA would probably have an easier time integrating this program into EteRNA. The benefit of actually seeing much more clearly how a design failed in lab, would possibly give us valuable hints as to why, and possibly help choosing betters mods.
Try to make it to the next dev chat, eternacac, and if you can’t, I’ll make sure to bring this up.