BIO_Mapper matlab tools for analyzing RNA hairpin folding pathways
(please check Contents.m)

Requirements: 

1) Matlab toolbox MATLAB_BGL 2.0
(http://www.mathworks.com/matlabcentral/fileexchange/10922)

2) Graphviz (http://www.graphviz.org/)

[Commands files]
  encode55.m, mapper_mst.m (using Matlab_BGL), writeDotFile.m (using
Graphviz), px_euclid.m, load_unfold.m, load_refold.m, examp_unfold.m,
examp_refold.m
   
[Data]
  trajs_refold.mat, trajs_unfold.mat.

[Examples] 

1) reproduce mapper graph for unfolding pathways in Figure 3(a):

  >> examp_unfold.m 

2) reproduce mapper graph for refolding pathways in Figure 3(b):

  >> examp_refold.m

[Reference]  
 Topological Methods for Exploring Low-density States on Biomolecular
Folding Pathways, by Y. Yao, J. Sun, X. Huang, G. Bowman, G. Singh, 
M.
Lesnick, V. Pande, L. Guibas and G. Carlsson, 2008.