Parallel detection of regulatory elements with gMP

The detection of regulatory elements from a large set of regulatory regions is a challenging problem in computational genomics. However, computational methods to extract this biologically meaningful information suffer from high computational requirements. In this paper we present a parallel algorithm to detect regulatory elements using correlation with gene expression data and its implementation with gMP. gMP is a new purely Java-based interface that adds MPI-like message-passing and collective communication to the genomics Research Network Architecture (gRNA). The parallel implementation leads to significant runtime savings on our distributed gRNA system.