For a tough RNA problem try Tuffy

Tuffy:Scaling up Statistical Inference in Markov Logic Networks using an RDBMS.

http://hazy.cs.wisc.edu/hazy/papers/t…
http://hazy.cs.wisc.edu/hazy/tuffy/do…

Best state of the art. Can it be applied to EteRNA?
We have massive databases and getting bigger everyday. The techniques used may be used by EteRNA in other ways too.