Theoretical Biochemistry Group

Institute for Theoretical Chemistry

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RNAlocmin program

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 KucharĂ­k, Ivo L. Hofacker, Peter F. Stadler and Jing Qin
Bioinformatics 2014

Supplementary material to the publication above can be downloaded from here.


New release 2.0 is out!!! Added support for pseudoknots (actually a class called 1-structures). [11-05-2015]

Known bugs

The --noLP option is not working properly. The bug is deep in the move_set routines in ViennaRNA package. We are working on a fix.


The latest stable release is v2.0 and is provided as a source code zip file:
RNAlocmin v2.0 (zip, SourceCode) [45.6kB]

Old version v1.0:
RNAlocmin v1.0 (zip, SourceCode) [29.2kB]

You can also watch latest releases on GitHub: RNAlocmin GitHub!


In case of problems, found bugs, or need to chat, do not hesitate to contact us: -- programming -- ideas