Parallel Algorithm for Multiple Genome Alignment on the Grid Environment

Nova Ahmed, Yi Pan, Art Vandenberg, Yuzhong Sun

Abstract: The multiple genome sequence alignment problem falls in the domain of problems that can be parallelized to address large sequence lengths. Although there is communication required for the computation of the aligned sequences, the proper distribution can reduce the overall problem to a set of tasks to be solved independently and then merged. A parallel algorithm for the alignment of multiple genome sequences is described. The algorithm is experimentally evaluated in a distributed Grid environment that provides very scalable and low cost computation performance. The Grid environment is evaluated with respect to a traditional cluster environment and results are compared to evaluate the effectiveness of a Grid environment for large computational biology.