Smith-Waterman Algorithm in OpenMP

A highly efficient and simple implementation of the Smith-Waterman algorithm for local alignment of sequences.

Sample Output

How to Use

Serial Version

• Compile the project

  gcc serial_smithW.c -o serial_smithW -fopenmp -DDEBUG

• Run the program:

  ./serial_smithW <number_of_col> <number_of_rows>

Parallel Version

• Compile the project

  gcc omp_smithW.c -o omp_smithW -fopenmp -DDEBUG

• Run the program:

  ./omp_smithW <number_of_threads> <number_of_col> <number_of_rows>

Bug Reports & Feature Requests

You can help by reporting bugs, suggesting features, reviewing feature specifications or just by sharing your opinion. Use GitHub Issues for all of that.

To do

• Display the result in a more user-friendly way.
• Make speedup tests to show how OpenMP accelerated the code.
• Add documentation about the diagonal approach used to implement the parallel algorithm.

Contributing

1. Fork the project.
2. Create a branch for your new feature.
3. Test your code.
4. Submit a pull request.

All pull requests are welcome !

Authors

This project was develloped by Daniel Holanda, Hanoch Griner and Taynara Pinheiro.

License

This project uses the MIT license. See LICENSE for more details.