A Profile Hidden Markov Model Generating and testing application developed towards completion of requirements for CS123B - Intro to Bioinformatics II as a course project.
Installations: requires python2
Steps to run:
Download the files and extract them use the following command to run the model:
python pyHMM.py Algined_nifH_Training.fa.txt model.json
Known Issues:
- some logical issues in implementation of viterbi algorithm producing erroeneous results
Still to do:
- Fix viterbi and FA implementations
- make model generation more robust
Contact: saketh.saxena@sjsu.edu in case of issues