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Sequence analysis Gene-IT emerges from stealth with analysis tools, customers


What do you get when you combine elements of the French contribution to the Human Genome Project and a founder of Blackstone Computing? Gene-IT, a sequence-analysis tool provider based out of Paris and Boston.

CEO Ron Ranauro says Gene-IT was founded in 1998 in France based on some of the technology developed by French genome institute INRIA to do “collaborative, comparative genomic studies with pharma and some of the research centers in Europe.” Gene-IT emerged as a way to commercialize some parts of that core technology, he says.

That technology is now a Google-esque approach to sequence retrieval and analysis. Using the DNA sequence itself as the primary index — “It’s the only reliable index,” Ranauro says, pointing out the problems of indexing by gene or protein names — the tool combs through its databases to come up with “the best-fit answer,” he adds. A user would “paste in entire lists of genes or sequence identifiers. [The GenomeQuest tool] would instantaneously retrieve them, then cross-reference that list with new information identified by sequence.” This could be used, for instance, for a list of genes expressed in a microarray experiment. To find the transcripts associated with those genes, the researcher would plug in “a list of microarray identifiers, generate a list of genes, and then cross-reference those lists to the transcriptome,” Ranauro says. The results would come back as “the best-fit answer from a list of 10 or 100 or 1,000 possible hits.”

For business reasons, the GenomeQuest application was initially targeted at IP researchers trying to find out whether something should be patented or whether a new discovery infringes on someone else’s IP, for example. “We found that where the rubber meets the road for a commercial research effort is in the intellectual property office,” Ranauro says. The tool was launched in January 2004, and during the last 18 months, Ranauro adds, “we’ve been quietly acquiring new customers” — an average of two new clients each month.

But the scientific research scene isn’t far off in the business plan. “There’s a need to deliver this functionality into the labs themselves,” Ranauro says. “We’ll be launching very focused solutions aimed at the end user biologist; for instance, validating siRNA probes.” Scientists currently relying on common solutions like NCBI Blast or Oracle are “essentially getting a static HTML result that [has to] be printed and filtered with human effort,” Ranauro says.

The company will continue to add new features and uses to the technology as well as more hooks to plug into other applications, says Ranauro, who helped found Blackstone Computing several years ago. “A lot of customers want to know if we’re going to do pathways or ontologies or systems biology or expression,” he says. “What we’re trying to say is the sequence reference data is the foundation for all of that.”

— Meredith Salisbury



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