Smith-Waterman algorithm
Usage: python local_align.py [gap cost] [gap extension cost] ['matrix name'] [Want only score?: True or False]
Part 1 --Implement/comment/test Smith-Waterman algorithm --Find best gap opening/extension penalty combination for BLOSUM50 --Compare ROC curves for matrices --Compare ROC curves for normalized and unnormalized scores Part 2 --Implement/test and describe optimization algorithm --Optimize starting from best matrix --Optimize starting from MATIO --Explain how to convincingly argue for utility of an optimized matrix