[Solved] Module 2 Assignment 605.451 Principles of Computational Biology

Small Project 1

1. Find the best local alignment between the following two sequences using two ways:
   1. Manually calculate scores on the DP table, draw the path, and write out the two aligned sub sequences. (50 points)
   2. Write a computer program in Java or any other programming languages to compute the local alignment score and print out the aligned two sub sequences. (50 points)

Q: GCTGGAAGGCAT

P: GCAGAGCACG

Linear gap model:

Gap = -4

Match = 5

Mismatch = -4

What to turn in

• Turn in DP table with the scores and paths
• Turn in the two aligned sub sequences
• Turn in your source code
• Turn in the output from your program