The program RNAlocmin reads secondary structures to RNA sequence provided in file seq.txt (can be altered with "-s" option) and search for a local minima by performing a gradient walk. These structures for input can be obtained with RNAsubopt program (part of the ViennaRNA package). RNAlocmin outputs energetically sorted list of local minima with their energies and number of hits to particular minimum, which corresponds to a size of the basin. Additional output, as for example barrier tree constructed with findpath method, Arhenius rates for kinetics and so on, can be obtained with use of additional flags.
For compiling RNAlocmin, you will need ViennaRNA package installed on your computer (tested with version 2.1.8).
Then follow instructions in README.txt bundled with program. Run
./RNAlocmin -h to get help and available options.
In case you are using our software for your publications you may want to cite:
Basin Hopping Graph: A computational framework to characterize RNA folding landscapes
Marcel Kucharík, Ivo L. Hofacker, Peter F. Stadler and Jing Qin