Genome 540 Homework Assignment 8

Due Sunday Mar 7

• Using the same HMM and dataset as in homework 7, write a program that implements EM (Baum-Welch) training instead. Use the same starting parameter values. Compute the log-likelihood of the sequence at each iteration, and run the program until the increase in loglikelihood between successive iterations becomes less than .1. You should check that the loglikelihood increases with each iteration -- if it doesn't, something is wrong with your program.
• Your output should provide
  • the name and first line of the .fna file
  • the number of iterations until convergence
  • the final loglikelihood
  • the final emission and transition probabilities
• Email the output above to me and Chris. Please make it as compact as possible. Do NOT send the code itself. Include the output in the body of your email message (as plain text), NOT as an attachment.