OSU researchers utilize TimeLogic DeCypher® at OSC to speed horse gene identification
Carlsbad, CA and Columbus, OH - Using the DeCypher biocomputing solution from TimeLogic deployed at the Ohio Supercomputer Center (OSC), Dr. Alicia Bertone of The Ohio State University (OSU) School of Veterinary Medicine and Dr. Weisong Gu, OSU postdoctoral researcher, have developed the first equine microarray featuring 3,800 genes.
"Through microarray analysis, we can study the regulation of the animal's entire genome under different environmental and disease conditions," said Bertone. "We utilized OSC's TimeLogic DeCypher system for large BLAST sequence comparisons of equine Expressed Sequence Tags (ESTs) with human and mouse genome databases to identify optimal gene sequences for microarray chip development."
"This is the first time we've been able to apply functional genomic studies to a large mammal, and believe the technique will enhance our understanding of human orthopedic diseases such as osteoarthritis," Bertone continued.
Dr. Eric Stahlberg, OSC Senior Systems Manager, remarked, "The DeCypher system is installed within the Sun Center of Excellence for High Performance Computing Environments and processes hundreds to thousands of sequence analyses per day." Stahlberg continued, "The DeCypher system processes high-speed bioinformatics analyses through parallel algorithm implementations on Field Programmable Gate Array chips, providing a modern, cost-effective resource for genomics researchers at OSU and throughout Ohio."
Gu compared thousands of sequences from horse to the GenBank sequence database at the National Center for Biotechnology Information (NCBI). "Comparing the horse ESTs to GenBank used to take several hours on my desktop workstation, which made repeating the analysis for each new release of GenBank too time-consuming. Using the TimeLogic DeCypher system, I now complete the searches in under 10 minutes, so our data stays current."
"TimeLogic's goal is to deliver genome-scale sequence analysis capability to researchers through our modular DeCypher biocomputing platform. We are very pleased to be expediting innovative research through OSC's DeCypher system," commented Joseph Fernandez, CEO for TimeLogic Corporation and parent company Active Motif. "As Dr. Bertone's research staff begins exploring horse protein functional classification, we expect that DeCypher's hidden Markov Model profile analysis tools will be highly valuable," Fernandez added.
TimeLogic produces the DeCypher solutions for genomic sequence analysis and protein functional annotation. DeCypher employs high-speed, reconfigurable computing technology to accelerate critical bioinformatics methods including BLAST, Smith-Waterman and Hidden Markov Model analysis. By deploying scalable, high performance computing systems within individual computing workstations, TimeLogic helps researchers utilize comprehensive techniques for gene and drug discovery efforts. TimeLogic is a wholly-owned subsidiary of Active Motif, which produces cell biology research tools for determining the functions, interaction and regulation of proteins.
OSC is Ohio's high performance computing and networking center. Established in 1987 by the Ohio Board of Regents, the Center provides scientific computing, networking, educational outreach, and information technology resources to state and national high performance computing and networking groups. OSC empowers its academic, industrial, and government partners to make Ohio the education and technology state of the future. For more information, go to www.osc.edu.