Skip to main content
Premium Trial:

Request an Annual Quote

PE Endorses Gene Codes Sequencher Tool with New BioLIMS Interface


ANN ARBOR, Mich.--Bioinformatics software company Gene Codes has already managed to corner the DNA-sequence-assembly market with one product and nary an outside sales rep. Now, with the promise of endorsement from Perkin-Elmer's expansive North American salesforce, Gene Codes' outlook is brighter than ever.

To satisfy customers who wanted a way to assemble data being generated by its sequencing machines, including the new Windows NT-based ABI 3700, Perkin-Elmer's PE Biosystems unit has asked Gene Codes to develop an interface between its sequence-assembly and contig-management software, Sequencher, and PE's sequence data management system, BioLIMS.

Howard Cash, president of Gene Codes, explained that, until now, users could only apply Sequencher to flat files taken from sequencing instruments that were then stored individually in BioLIMS. Or, customers of earlier, Macintosh-driven models--the ABI 310, 373, and 377--could employ Perkin-Elmer's own sequence-assembly software, AutoAssembler.

But recent market research undertaken by Perkin-Elmer revealed that its customers preferred Gene Codes' product, which has long been available for the Macintosh and was released in a Windows version last year. One BioLIMS salesman told Cash that he's never made a sales call when he hasn't been asked if the product can be used with Sequencher. Now, every BioLIMS sold will be Sequencher-compatible. Cash said the deal makes Gene Codes the first third-party, commercial developer to be certified to work with BioLIMS.

In terms of marketing power, the deal is like a big bang for Gene Codes, which has relied solely on display advertising, scientific conferences, and direct mail to market its products. "We don't have Gene Codes employees walking the halls and knocking on lab doors," said Cash. "We went from a company with no field staff to one with 200 representatives in North America alone." Cash has been invited to train Perkin-Elmer's national salesforce, which will recommend Sequencher not just as a complement to BioLIMS, but also as standalone software.

DNA pickaxes

Arguably the most popular commercially available desktop sequence assembly program, Sequencher already has more than 6,500 users worldwide, including most major universities and practically every pharmaceutical company in the world. To what does the company attribute its success? "Fragment assembly is a computationally difficult problem, and we found a way to solve it very efficiently," said Cash. Speed and accuracy have been key to having a viable product, too, he added.

But Gene Codes' staying power is in the combination of Sequencher's scientist-friendly design and extraordinary customer service, Cash contended. "We give customer support over the phone, web, or email, but it often means going as far as adding FEATURESthat particular customers need," he said. For instance, when Richard Kolodner at the Dana Farber Cancer Institute located the MSH-2 colon cancer gene and needed to produce a figure for publication in Cell, Gene Codes wrote a one-off version of the program for him. Its engineers also added Genentech's proprietary file format to Sequencher's export option, "even though, clearly, there are not other customers who will use it," remarked Cash.

Despite having already captured a chunk of the market, Cash, who is one of 11 investors in the privately held firm, sees plenty of room to expand. Gene Codes has grown at least 25 percent every year since it was incorporated in 1988, he claimed. In the coming fiscal year, with PE's support, he expects to grow "substantially more than that."

To describe his company's prospects, Cash has adapted the oft-used genomics-revolution-as-gold-rush analogy: "In the gold rushes in Northern California and Alaska, some people struck gold and became rich, and a lot of people washed out. But the class of people that consistently did well were those who made pans and pickaxes." Gene Codes, he said, makes pickaxes for this gold rush. As throughput gets higher and costs lower, more sequencing will get done and data management demands will increase, he noted, adding, "And we get more customers."

--Adrienne Burke

Filed under

The Scan

Booster for At-Risk

The New York Times reports that the US Food and Drug Administration has authorized a third dose of the Pfizer-BioNTech SARS-CoV-2 vaccine for people over 65 or at increased risk.

Preprints OK to Mention Again

Nature News reports the Australian Research Council has changed its new policy and now allows preprints to be cited in grant applications.

Hundreds of Millions More to Share

The US plans to purchase and donate 500 million additional SARS-CoV-2 vaccine doses, according to the Washington Post.

Nature Papers Examine Molecular Program Differences Influencing Neural Cells, Population History of Polynesia

In Nature this week: changes in molecular program during embryonic development leads to different neural cell types, and more.