Source Code and Data for RNApathfinder
- greedyPathMorganHiggs.py:_ Morgan-Higgs greedy algorithm.
- Morgan-Higgs Indirect: extension of Morgan-Higgs method to Turner energy model.
- freqStrInPaths.py: Program finds frequencies of different structures in output from web server.
- bestPath.py: Program finds best path among those output from web server.
- Density plots from RNAbor to determine meta-stable structures.
- Best pathway for found by the Morgan-Higgs indirect, semi-greedy and TABU semi-greedy methods for various conformational switches described in article: Morgan-Higgs indirect, semi-greedy, TABU semi-greedy.
- findPath: accesses the Vienna subroutine findPath, to allow for comparison to RNApathfinder
Saddles: List of saddle points for analyzed
If you use the source code below please cite:
I. Dotú, W.A. Lorenz, P. Van Hentenryck, P. Clote. Computing folding pathways between RNA secondary structures. Nucleic Acids Res. 2010 Mar 1;38(5):1711-22.
- TABU source code: When using, try with
minimum weight wMin of 10 and maximum weight wMax of 70.
These were the weights used in benchmarking experiments for the article
cited above. Note that there
is a typo on page 1718 of this article, right side, first paragraph
of Results: "Reported values were for wMin = 1 and wMax = 7,
which are the default values on the web server." This should
be corrected to "wMin=10 and wMax=70.