Chunks and Tasks sample code -- Smith-Waterman sample
This example program demonstrates how the Smith-Waterman algorithm can be implemented using the Chunks and Tasks model.
The Smith-Waterman algorithm is a bioinformatics algorithm that performs local sequence alignment, for e.g. finding similarities in DNA or RNA sequences. The implementation in the sample code given here is for the simple case of a linear gap model, following the definition given here.
For simplicity, the sample code requires the length of the input sequences to be a power of 2. A few small test sequences are provided in the test_data directory in the sample code .tar.gz file. The program expects two input arguments, giving filenames for the two sequences that are to be aligned.
Download the source code for the Smith-Waterman sample program using this link:
sample-smith-waterman.tar.gzTo compile and run the program, a Chunks and Tasks library implementation is needed. See the Library implementations page for descriptions of how to compile and run the program using the library implementations available there.