University of Virginia
Dynamic Programming, Bioinformatics
Needleman-Wunsch is a nonlinear global optimization method for DNA sequence alignments. The potential pairs of sequences are organized in a 2D matrix. In the first step, the algorithm fills the matrix from top left to bottom right, step-by-step. The optimum alignment is the pathway through the array with maximum score, where the score is the value of the maximum weighted path ending at that cell. Thus, the value of each data element depends on the values of its northwest-, north- and west-adjacent elements. In the second step, the maximum path is traced backward to deduce the optimal alignment.
Input is the number of rows/columns, penalty, opencl file and times to loop kernel. Data is set internally to the requested conditions.
Output is the traceback of the generated path.
The output file nw.out contains detailed timing information about the run. It also shows which device was selected along with what devices where available to OpenCL.
 S. Che, J. W. Sheaffer, M. Boyer, L. G. Szafaryn, L. Wang, and K. Skadron. A Characterization of the Rodinia Benchmark Suite with Comparison to Contemporary CMP Workloads. In Proceedings of the IEEE International Symposium on Workload Characterization, Dec. 2010.