BSE322A - Bioinformatics & Computational Biology

Programming Assignment

Dated: 29th March 2018
Rohit Gupta (150594)

Algorithm Implemented : Local Alignments in sequences with Affine Gap Penalty

Input Format -

• Line 1 : match_reward mismatch_penalty gap_start_penalty gap_continuation_penalty
• Line 2 : sequence 1
• Line 3 : sequence 2

Output Format -

• The code outputs all details along with local alignments at stdout.

Running instructions -

Run the following commands to get alignments from input1.txt(in folder input).

make
./align < input/input1.txt

NOTE : The program does not output all possible optimal local alignments. It outputs an optimal alignment for each occurence of max_score in scoring matrix.