Command Usage

./kmerHMM inFilePath outHMMfilePath kmerLength numOfStates tol

Input Arguments:
inFilePath: The input probe file path (example: Cbf1_deBruijn_v1.txt)
outHMMfilePath: The output HMM model file path (default: kmerHMMmodel.mat)
kmerLength: The length of k-mer used(default: 8)
numOfStates: The number of hidden states (default: 50)
tol: The tolerance used for testing convergence (default: 0.001)

Output Files:
A HMM model file (example: kmerHMMmodel.mat)
Direct and Reverse Complement sequence logo PNG files for the most probable state paths (example: Cbf1_deBruijn_v1.txt.png)



MCR (Matlab Compiler Runtime)
kmerHMM files (zipped)


Source Codes

For source codes and potential collaborations, please contact Ka-Chun Wong



Please note that the example data is generously provided by UniProbe. Please cite and acknowledge them if you use it. More PBM probe data can be found in UniProbe


© 2013 Ka-Chun Wong | Template design by Andreas Viklund