Myriad Proteomics Implements TimeLogic DeCypher to Accelerate Analysis of Human Proteome Data

DeCypher improves value of proteomics data and extends capability of Sun Microsystems servers

Through their unique and comprehensive approach to protein characterization, Myriad Proteomics is developing a better understanding of human biochemical pathways. The daily workflow generates a tremendous volume of DNA and protein sequence data. Myriad Proteomics has selected TimeLogic's DeCypher system for the demanding computational analysis of these sequences. The system will help their scientists discover interactions between proteins in order to fully characterize and validate potential targets for therapeutic intervention.

"To process and interpret protein interaction data, we analyze both nucleotide sequences collected from the yeast 2-hybrid workflow and protein sequences from the mass spectrometry workflow. We have to piece together hundreds of thousands of DNA fragments to identify where in the human genome the interacting sequences can be mapped to and what alternatively spliced form they are in. We also have to perform large-scale protein sequence analysis using sensitive multiple sequence alignment and domain search methods", explained Jake Yue Chen, Ph.D., Head of Computational Proteomics at Myriad Proteomics. "The DeCypher system's capacity for running algorithms optimized for protein sequence analysis ultimately brings a great advantage to the project", he added.

"DeCypher processes bioinformatics searches at high speed—hundreds to thousands of times faster than a single server—through the use of Field Programmable Gate Array (FPGA) computing technology. The system automatically loads a virtual "algorithm chip" at runtime, and reconfigures instantaneously when a different algorithm is required," commented Christopher Hoover, Marketing Manager for TimeLogic. "DeCypher's reconfigurable nature leads to a space-efficient and low power design, and allows TimeLogic to distribute new features through software updates, extending the lifespan of the equipment."
Sami Kergaye of Myriad Proteomics IT Systems, remarked, "The DeCypher system, implemented within a Sun Microsystems V880 server, compressed our Hidden Markov Model [HMM] searches from 9 hours to less than 5 minutes. This greatly extends the utility of our Sun server and enables us to rapidly evaluate data as it is generated."

"A deeper understanding of the human proteome strengthens the potential of Myriad Proteomics' data for their pharmaceutical partners," commented Rick MacDonald, President and CEO for TimeLogic. "TimeLogic is pleased that DeCypher's acceleration technology will help Myriad Proteomics achieve a comprehensive view of human protein interactions, which will offer tremendous potential for discovery of novel drug targets and unique lead compounds for drug discovery."

About Myriad Proteomics, Inc.
Myriad Proteomics Inc., a private company, is a leader in employing mass spectrometry and yeast two hybrid technologies in a high throughput production environment to discover and analyze protein interactions. Myriad Proteomics intends to utilize its proprietary technologies and processes to define a comprehensive human protein interaction map and, in combination with high throughput screening and validation techniques, to enhance protein-based drug discovery working with partners in the pharmaceutical industry. The Company maintains its principal offices and laboratories at 2150 West Dauntless Ave., Salt Lake City, Utah 84116.

About TimeLogic Corporation
TimeLogic produces DeCypher, a leading edge solution for accelerating life science computation—including BLAST, Smith-Waterman and Hidden Markov Model analysis—utilizing high-speed, reconfigurable FPGA technology housed in a standard server from Sun Microsystems. The system speeds 35 critical genomic research tasks, and enables compound research techniques to be employed for more comprehensive scientific results. DeCypher is utilized by top biotechnology, pharmaceutical, and agribusiness companies, as well as academic and government research institutions worldwide. TimeLogic has been accelerating bioinformatics discovery since 1996. Media contact: Christopher Hoover, Marketing Manager, 760-431-1263, hoover@activemotif.com, http://www.timelogic.com

Sun, Sun Microsystems and the Sun logo are trademarks or registered trademarks of Sun Microsystems, Inc. in the United States and other countries. DeCypher is a registered trademark of TimeLogic.

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[pdf version of this release]

Media Contact
For company information, please contact:

Christopher Hoover
Marketing Manager
Phone: 760-431-1263
Email: hoover@activemotif.com

LifeSeq is a registered trademark of Incyte Genetics
DeCypher is a registered trademark of TimeLogic Corporation.

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