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SLIM Down Your Blast, Fast


By Jennifer Crebs

The prospect is ridiculously attractive: Imagine running a fully optimized Blast search at a rate 10,000 times faster than its usual lumbering stride, without souping up your machine with specialized hardware. That’s exactly what Leonard Bloksberg aims to provide with his company’s latest technology, SLIM Search.

“SLIM Search works [by returning] richer data content that makes it possible to create scores and molecular alignments directly from a word search,” Bloksberg says. It also “digitally tags the alignments so subsequent analysis can be computerized and automated for the first time.” Scalable, efficient searching at a speed Bloksberg claims means that specialized hardware can be freed up for tasks “more interesting” than the daily grind of sequence searches.

SLIM, an acronym for Sequence Location Indexer and Matcher, is the technology that forms the core of SLIM Search. The software is being commercialized by Cartesian Gridspeed, a bioinformatics startup that Bloksberg founded in April 2005. Before launching the company, Bloksberg worked as a senior scientist at Genesis Research, a New Zealand-based biotech firm where the first incarnation of SLIM was developed.

The key to SLIM Search’s performance, he says, is the way in which it builds and scans an array for exact matches of some defined length. “Modern genomics search tools break a search into two steps: a word search followed by an alignment,” says Bloksberg. SLIM Search improves on the word search phase, using the same alignment process as Blast to generate data in a familiar format. “The end result is the same,” Bloksberg says, noting that “an exact match of 11nt does not vary no matter how you found it.”

Users need no specialized setup to get started with SLIM Search — the software requires only Java 1.5. The current release has been tested on and is fully supported by AMD and Intel chips; Microsoft and Linux operating systems; and 32-bit and 64-bit setups. Bloksberg says that the company plans to expand support as the market demands.

At Genesis, Bloksberg was involved in compute-intensive systems biology research. Development work on the SLIM technology began when it was estimated that it would take 20 years to complete the systems-level analysis of a forestry genome using a top-of-the-line CPU. Bloksberg’s team at Genesis struck up a collaboration with local programmers working for a US-based bioinformatics firm, and the SLIM technology was born. With the tool, the original problematic search took only nine hours on a Pentium III.

When Genesis began handing out pink slips in 2004, right around the time several of its drug candidates failed phase II trials, Bloksberg found himself out on his own. He decided to acquire the SLIM technology and build a company to market it, orchestrating his programming team’s efforts to implement tweaks to make SLIM Search capable of running faster and more sensitive searches than was possible at Genesis. Over the past year, Cartesian Gridspeed’s in-house staff of four has worked with several contractors to develop a commercial-ready version of the software. Later this year, Bloksberg expects to expand his global sales and support staff.

An early release version of the software was tested by several companies in New Zealand, and beta testing commenced internationally earlier this year. Among customers in the US who have already signed on for a license, Cartesian Gridspeed counts both Agencourt and Cold Spring Harbor’s James Watson School of Biological Sciences. Users in the beta program are encouraged to run comparisons of SLIM Search with other tools, Bloksberg says. He adds that customers are welcome to publish the results from such studies as well.

 “It is important to us that each of our test sites is doing unique and novel research with SLIM Search, and our current users reflect this,” Bloksberg says. If the benchmarks are any indication, once the market-ready version of the product is ready this fall, more novel and unique applications shouldn’t be too far behind.

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