First released in 1991, Sequencher has become the industry standard for DNA sequencing, and was an important tool in the early stages of the Human Genome Project. Indeed, some of M-FISys was based on Sequencher, but it was mostly built from scratch. The company, which was founded by Cash in 1988, has also created software used by the U.S. Army and the FBI for identifying old war remains and helping the government use DNA samples to identify criminals.

Gene Codes was profitable for 39 consecutive quarters before embarking on M-FISys. Cash set up Gene Codes Forensics Inc., a wholly owned subsidiary of Gene Codes, to create M-FISys, while protecting the rest of the company's assets. Gene Codes signed a three-year, $10-million contract with New York City but will bill for only real hours and expenses — already close to $7 million.

"We made a decision early on not to try to profiteer on this project," Cash says. "We honestly thought we would be working on this for a year at the most." The company will probably see some paper profit eventually, but that will compensate for losses incurred by the pause in Sequencher development. "You don't make money selling software, you make money selling upgrades," Cash says.

Sales manager Carol Carriere says the company "knew it would put a strain on [Sequencher] sales, but the real loss wasn't financial. We lost time for development, and that gave our competitors a chance to catch up."

Even though it will take time before most staff members can refocus their efforts on Sequencher, Cash has no regrets. "If in the process we had brought some comfort to these hundreds and hundreds of families, but in the end we had lost the company, I would still have thought we had made a good investment and the right decision."

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