Project 4: Viterbi algorithm


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Project 4: Viterbi algorithm for protein family profile HMM alignment
Objective: Implement the Viterbi algorithm for protein family profile HMM alignment. You only
need to implement the global version.
A. Input format
The format of the first input of the program, is the query profile HMM. You can download as an
example a profile HMM file from For more detailed
instructions of the file format please see
(page 106).
The second input of the program is a FASTA file. It contains a single sequence. Please refer to
HW1 for more detailed discussions on its format.
B. Output format
The output of the program is similar to that of HW1, except the following differences:
• 1: The score is the likelihood of the Viterbi path rather than the alignment score;
• 2: The sequence of the profile HMM is determined by the match-state characters that have
the highest emission probability;
• 3: Use ‘+’ to indicate a positive match if the emission probability of the matched character
(in the target) in the matched state is higher than the background frequency of the matched
C: Test case
You are encouraged to check your result using HMMER3. You can download HMMER3 at Detailed manual and instructions can also be found from the website.
D: Submission
• Please submit your source code via Blackboard by April 30th 2021.
• Include a README file describing how to run your program.

Project 4: Viterbi algorithm
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