Description

Assignment #2
Written Assignment

In this assignment, your goal is to construct a profile Hidden Markov Model (pHMM) for the following 8 DNA sequences using their multiple alignment given below and then align a new sequence to the constructed model using the Viterbi algorithm.

–TT–GA-G—
TATT–CAC-A
-CATGGCA–—
GC-T—ACGA
–GT–CT–—
GC-GT-CT–—
-C-T–CA-G— * * **

Part B: Align the following sequence to the profile HMM using the Viterbi algorithm. In other words, find the sequence of states which is most likely to emit that sequence. Show the contents of the partial probability table you construct. What is the probability associated with the best path?

AATGAC

Submission: