Homework Assignment #2

Due Thursday, 10/15, 11:59pm

Substitution matrix

BLOSUM-62 substitution matrix file. You can assume that any substitution matrix given to your program will be in the same format as this file.

Sample input/output

You may wish to test your program with the following inputs/outputs. The output is the correct alignment given the BLOSUM-62 substitution matrix, g = -10 and s = -1.
  1. simple example: input, output
  2. calcium ion proteins: input, output
  3. yeast kinase proteins input, output
Additionally, we will test your programs on several held-aside sequence pairs.