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Paradigm Strengthens Bioinformatics Base By Partnering With Paracel, PE Biosystems

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RESEARCH TRIANGLE PARK, NC--Paradigm Genetics has recently signed two deals that will significantly strengthen the bioinformatics component of the year-old agricultural genomics company's R&D efforts.

Last week Paradigm announced that it has installed a GeneMatcher genomic analysis system, the latest product from Pasadena, Calif., bioinformatics firm Paracel, to enable high-throughput gene annotation. Earlier in May, Paradigm signed a five-year deal with Perkin-Elmer's PE Biosystems Group to jointly develop bioinformatics software for use in functional genomics applications. As part of the arrangement, Paradigm acquired PE's SequelGT, BioLIMS, and BioMerge database architecture tools.

John Ryals, Paradigm's CEO, told BioInform the computational enhancements will be employed to construct AgDB, an agricultural genomics database.

Craig Liddell, Paradigm's informatics director, said Paracel's massively parallel data analysis engine, which contains more than 6,000 custom processors, programmable to execute algorithms such as Smith Waterman, hidden Markov models, and frame and profile searches, will allow Paradigm to conduct searches that previously would have been impossible. "It enhances our ability to identify agriculturally important genes that will be used in a new generation of highly specific and safer agricultural products," Liddell said.

Ryals, who was formerly head of ag biotech research at Novartis, said Paradigm is designing AgDB to "become the powerhouse of the industry in terms of gene function analysis." Instead of licensing the database, Paradigm intends to use it as a discovery tool in partnerships, such as one it has for herbicide product development with Bayer.

Paradigm's plant genomics knowledge is also attractive to bioinformatics firms. "We're out there doing rapid functional analysis with plants and fungi," explained Ryals. "We can go faster than pharmaceutical companies, so companies like Paracel and PE see that as an advantage for finding out what's coming two or three years down the road in the pharmaceutical industry."

Kwang-I Yu, Paracel's CEO, called Paradigm's incorporation of advanced technologies impressive. "They represent the beginning of an exciting new era in the application of genomics to improving agriculture," he said.

Product development partnership

Its arrangements with both PE and Paracel call for Paradigm to contribute to bioinformatics product development. With Paracel, Ryals said, "the intent is more than to install the box." GeneMatcher has the potential to do a number of different types of computational analyses, he said, and Paradigm will share its ideas about how to modify the instrument.

With PE Biosystems, Ryals said, "we'll be participating in designing and altering software and databases," which will include providing large datasets that PE can use to test new components.

Bob Jones, vice-president and general manager of PE Informatics, told BioInform the products that result from the collaboration will be equally applicable to the pharmaceutical industry. Agreeing with the assertion that bioinformatics tools are generally applicable across the two industries, Jones explained, "I would say the differences have to do with the kinds of experiments you can do on plants that you can't do on humans. That certainly affects how you do things such as hunting for genes and mapping experiments because you can do all kinds of crosses in plants. But other than that front-end part, I think things are very similar."

PE Informatics, according to Jones, targets each market that PE Biosystems addresses. "Consequently, agriculture is as important as pharmaceutical in the big picture," he said, but added, "Our focus is on the pharmaceutical market and we expect to be able to use what we do in that market."

--Adrienne Burke

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