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 biological 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.

• Type: Conference
• Year: 2003
• Where: IPPS
• Authors: Bertil Schmidt, Lin Feng, Amey V. Laud, Yusdi Santoso
• Keywords: Computational Genomics, Distributed And Parallel Computing, IPPS 2003, Regulatory Elements, Regulatory Regions