Software enables DNA comparison on 'regular PC'

Speed of algorithm allows for DNA comparison searches on regular PC

Software developed in Hamilton has been picked up by Microsoft US, providing the company, NetValue, with a great push into the US market.

Microsoft has made NetValue a partner in its High Performance Computing (HPC) programme, as well as in its High Potential Managed Independent Software Vendor (ISV) programme and its Life Sciences Partner programme.

As part of the High Potential Managed ISV programme, which only has 400 members worldwide, NetValue will be appointed a personal Microsoft architect evangelist and an account manager, to accelerate the adoption of NetValue’s software, SlimSearch, globally.

The SlimSearch software is a high-speed search and analysis tool for DNA, says NetValue’s chief executive, Graham Gaylard.

It allows researchers to rapidly search and compare various pieces of DNA or whole genomes — from bacteria to plants and humans — without the use of supercomputers, he says.

It enables, for example, comparisons of parents’ DNA with that of their children, he says. The company is currently part of a project that involves mapping the DNA of a child with that of her parents. The child has an undiagnosed genetic condition, and her father, Hugh Rienhoff, who is trained as a clinical geneticist, has been trying to find the answer for the last four years, says Gaylard.

Using the SlimSearch technology, it is possible to identify what genes the father and the mother have, and what genes the daughter shares, he says. Rienhoff has set up a website dedicated to expanding the understanding of genetic conditions and variations in the human genome, called

The speed of the algorithm also makes it possible to undertake DNA comparison searches using a regular PC, although it takes a little bit longer than using a cluster, says Gaylard. Mapping the father, mother and daughter took 30 minutes on a PC, but on a 60-node cluster it would have taken one minute, he says.

The driving force behind this technology is the evolution of next-generation sequencing machines, which can crunch masses of data, he says. The human genome is 4GB long, and to get the sufficient coverage you will need 12-20GB of data to process. DNA comparisons are very complicated, he says. But, using the SlimSearch technology, combined with Microsoft’s HPC Server platform, will allow a broader group of researchers to do comparisons in real-time.

Such developments are moving us towards personalised medical records that will store human genome information, allowing for DNA samples to be used for research, says Gaylard.

NetValue sent a sample of its software to Microsoft in November 2007, but it was not until May this year that the software giant reached out its hand.

“We got the big call out of the blue,” says Gaylard, who started out as an electrician before studying computer science and launching his career as an entrepreneur.

The technology, which was initially Linux and Java based, was developed by Dr Stuart Inglis, Dr Leonard Bloksberg and Professor John Cleary. NetValue and the original SlimSearch merged 18 months ago. The algorithms behind the tool were developed during a research and development project for Genesis Research and Development, in 2004.

Gaylard was in the US last week to raise venture capital funding to establish an office in California. He expects the research and development team in New Zealand to grow rapidly. The group of five that has been involved in the project will quite quickly expand to 20, he says. The company currently has 40 staff in total.

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Tags DNADevelopment IDnetvalue

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