Hi,
I'm looking for an tool, which can calculate the free energy of the most likely secondary structure of an short RNA sequence (50-100nt), for the developement of an R-package. The famous mfold tool unfortunately seems to complex to integrate it into an package (the authors are contacted). I want to automate these calculations independent of the internet and therefor cannot use the webserver.
For other parts of the package, I already integrated an Perl script, but mfold is just a little to complex, I think, for integration. Do you maybe know a script which does that kind of calculations, which does not require compilation or even another R-package, that already does it?
Any help is greatefully appreciated.
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ViennaRNA is the most widely used package I know of. It already has various wrappers/ports for integration in a number of languages - R may already be one of these (I know python is).
thank you very much! I did no see that after my initial quick readthrough and will definitly look into it.
Ok, so there is an R-package called LncFinder which can be used to apply ViennaRNA in R, in case someone is interested.