WaMoFi

WaMoFi: Is a method for finding protein motifs using the stored information from statistical contact potentials (aaindex) and the a representation by the continuous wavelet transform.

Please use: R 3.1.0 and Matlab 2014

How to use:

Just replace the directory and files In the head of the WaMoFi.m script. Then, run it in a matlab console.
--dataset: your data set in a fasta file
--labels: a file with the label/class per line
--percTest: how much of the test will be used for finding the motifs?. 0.7 means the 70% of the sequences in each class are used to find the motifs, whereas, the 30% are used to validate those motifs.
--outDir: directory where do you want the output
--SourceDir: where the WaMoFi files are stored in your machine.

This source run over any UNIX machine.

Requirements:

R packages:
pso, gplots, entropy, e1071, DMwR, kernlab, seqinr, pcaPP, flashClust, dynamicTreeCut.

TESTING:
see README file for details.