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RNAlocmin program

The program RNAlocmin reads secondary structures from standard input to an 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 the 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:

Marcel Kucharík, Ivo L. Hofacker, Peter F. Stadler, and Jing Qin
Basin Hopping Graph: A computational framework to characterize RNA folding landscapes
Bioinformatics 2014, doi:10.1093/bioinformatics/btu156, Supplementary material, ( bibtex)
Marcel Kucharík, Ivo L. Hofacker, Peter F. Stadler, and Jing Qin
Pseudoknots in RNA folding landscapes
Bioinformatics 2015, doi:10.1093/bioinformatics/btv572, Supplementary material, ( bibtex)


  • 18 - 12 - 2015

    New release 2.1 is out!!! Added an experimental version of Neighborhood routines, that can speed up the walking on RNA folding landscapes up to 4x.

  • 11 - 05 - 2015

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

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 Version 2.1.0

Get the source code and compile it yourself Compile from Source Code

Just download and install RNAlocmin using the sourcecode provided below.

RNAlocmin v2.1.0 (tar.gz, SourceCode) [49.2kB]

You can also watch latest releases on GitHub: RNAlocmin GitHub

Older versions:

There should rarely be a good reason to use any but the latest version of our software. However if you want to look up the old bugs, here's a list with most of the older releases for download.


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

  • -- programming
  • -- ideas
If in doubt our program is right, nature is at fault.
Comments and bug reports should be sent to