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:
Basin Hopping Graph: A computational framework to characterize RNA folding landscapes
Bioinformatics 2014, doi:10.1093/bioinformatics/btu156, Supplementary material, ( bibtex)
Pseudoknots in RNA folding landscapes
Bioinformatics 2015, doi:10.1093/bioinformatics/btv572, Supplementary material, ( bibtex)
News
-
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.
Download
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.
Contact
In case of problems, found bugs, or need to chat, do not hesitate to contact us:
- marceltbi.univie.ac.at -- programming
- qinbioinf.uni-leipzig.de -- ideas
Comments and bug reports should be sent to rna@tbi.univie.ac.at