rafftod / cpa2019

C/C++ implementation of Smith Waterman sequence alignment algorithm

CPA2019

C/C++ sequence alignment scoring using Smith-Waterman algorithm.

Compiling

After cloning the repository, run the following command :

make

The program is now compiled and ready to run.

Running the program

./main database_file query_protein_file_to_base_scores

This will run the program with default options:

• Gap open penalty : 11
• Gap extension penalty : 1
• BLOSUM matrix : BLOSUM62

The default output will be the top 20 sequence titles with their score.

Optional command-line parameters

You can customize penalties and BLOSUM matrix on which the algorithm is based.

./main database_file query_protein_file_to_base_scores [-o gap_opening_value] [-e gap_extension_value] [-b BLOSUM_matrix_file_path]

This line will launch the program with custom gap penalties and BLOSUM matrix. Make sure the BLOSUM matrix file exists in the given path.

All command-line parameters:

• -o gap_opening_value : sets the gap opening value to given argument.
• -e gap_extension_value : sets the gap expansion value to given argument.
• -b BLOSUM_matrix_path : sets the BLOSUM matrix to given path. Needs the matrix file to exist.
• -n N : restricts the database to N sequences.
• -s offset : sets the program to start at given offset in the database.
• -t top : sets the number of top proteins to be displayed.