Tool for calculation of free energy of most likely secondary structure of an RNA sequence

Question

[caggtaagtat]

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.

[Joe]

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).

[caggtaagtat]

thank you very much! I did no see that after my initial quick readthrough and will definitly look into it.

[caggtaagtat]

Ok, so there is an R-package called LncFinder which can be used to apply ViennaRNA in R, in case someone is interested.