The Smith-Waterman algorithm identifies the similar regions in two genome sequences. In this assignment, you will implement a Pthread version of the Smith-Waterman algorithm to measure the similarity between two strings.

The pseudocode of the Smith-Waterman algorithm is shown in Algorithm 1. Given string A = a₁,a₂,,a_n and string B = b₁,b₂,,b_m, we first construct a scoring matrix H of size (n + 1) (m+1) and set the first row and column to zero. Then, we iteratively compute the scoring matrix using the following dynamic programming formula:

where s is the substitution matrix is the match score, v is the

mismatch score, and w is the gap penalty. The value of u, v and w are constant and are given as part of the input to the algorithm. Finally, we return the highest score in the scoring matrix as the similarity score between A and B.

Input and Output

The input file will be in the following format:

1. The first line contains two integers a_len and b_len (1 a_len 20000,1 b_len 20000), separated by a space. They represent the length of string a and b, respectively.
2. The second line is a string a of length a_len, consisting of four letters A,T,G,C.
3. The third line is a string b of length b_len, consisting of four letters A,T,G,C.

Assignment 2 COMP5112, 2020 Spring

Algorithm 1: The Smith-Waterman Algorithm

Input : string A = a₁,a₂,,a_n and B = b₁,b₂,,b_m, match score u, mismatch score v, gap penalty w

Output: the similarity score between A and B

• int score[|A| + 1][|B| + 1];
• for i 0 to |A| do

3score[i][0] 0;

• end
• for i 0 to |B| do

6score[0][i] 0;

• end
• int max_score 0;
• for i 1 to |A| do
• for j 1 to |B| do

11score[i][j] max(0,

12score[i 1][j] w,

13score[i][j 1] w,

14score[i 1][j 1] + sub_mat(a_i,b_j));

15max_score max(max_score,score[i][j]);

• end
• end

The output of the program consists of two lines:

1. The similarity score between a and b, i.e., the highest score in the scoring matrix.
2. The elapsed time in seconds of the execution.

We assume that the match score is 3, the mismatch score is -3, and the gap penalty is 2.

Here is an example input/output for your reference:

Input:

9 8

GGTTGACTA TGTTACGG

Output:

13

Time: 0.00001 s