Gridification of the SHMap Biocomputational Algorithm

In the current study we present a parallel statistical algorithm (SHMap), which distinguishes DNA regions which possibly carry protein coding information from non-coding regions. The code was parallelized using MPI and was deployed in a Grid testbed provided by the CrossGrid IST European Project. We tested the SHMap algorithm on mammalian chromosomes. The paralleliza-tion of the algorithm and the use of the Grid environment achieves significant speed-up compared to the sequential version of the algorithm, although the use of the Grid environment still presents some problems. Our algorithm is open source and freely distributed from our website.