Cartesian Gridspeed, a bioinformatics startup based in Auckland, New Zealand, has released the beta version of a genomic search tool that it claims offers a 10,000-fold speedup over NCBI Blast.
The company, founded last April, has seven customers in New Zealand for the product, called SLIM (Sequence Location Indexer and Matcher) Search, but has just begun speaking to potential beta customers in the US, CEO Leonard Bloksberg told BioInform last week.
Bloksberg, fresh from a roadshow in the Boston area, said that he is seeing interest from potential beta customers once they get over their initial skepticism about the product's performance.
"The typical response is, 'Yeah, right,'" he said. "The hardest part is getting past that, but if they listen, they're usually impressed and ready to take a punt."
The key to SLIM's performance is the array in which the data to be searched is stored. "We re-engineered how the programming language builds and scans arrays," Bloksberg said. Blast is a two-step process, he noted a word-search step and an alignment step. SLIM Search tackles the first half of the process to speed up the word search, and then uses the same alignment method as Blast, called Bl2Seq, in order to generate the same statistics and gap penalties that researchers are familiar with.
In benchmarks with an all-by-all comparison of 5 million poplar genome reads, SLIM conducted 5 million searches with a word length of 30 in 2.5 hours on a single PC, while Blast conducted 1,000 searches with a word length of 11 in 5.7 hours on the same machine and SSAHA conducted 20,000 searches with a word length of 14 in 18 minutes. The company estimated that it would take 3.3 years for Blast to carry out all 5 million searches and SSAHA 3 days to do the same.
Bloksberg noted that SLIM slows down as its sensitivity increases, however, and when it is set to provide the same sensitivity as Blast for highly divergent sequences, it offers a 103-fold speedup.
Bloksberg said that he began developing SLIM as a senior scientist at Genesis Research, a biotech firm in New Zealand, when he was working on a systems biology experiment that would have taken 20 years to analyze on an HP ES40.
Researchers at Genesis began collaborating with programmers from Reel Two, a San Francisco-based bioinformatics firm with a development office in New Zealand, and came up with a prototype that reduced the time for the same search to nine hours on a Pentium box.
Last year, after several Genesis drugs failed Phase 2 trials and the company began laying people off, Bloksberg said that he found himself and his pet project "out on the street." So he sold his house, founded Cartesian Gridspeed, and convinced some additional investors to take a chance on the technology.
Over the last year, the company has worked with several contractors to develop a production-ready version of the software with a user-friendly interface, full documentation, help features, and installation wizards. Cartesian Gridspeed only has four full-time employees, but Bloksberg estimated that somewhere between 40 and 50 people are working on the product at any one time when outside contractors are accounted for.
If the beta program goes as planned, Bloksberg said that he hopes to launch SLIM Search 1.0 sometime in August. The product will initially be targeted at bioinformatics groups with fairly large compute clusters, so it will be priced at $399.95 per copy for enterprise-wide licenses of 100 copies or more.
Beta customers will receive the software free for 30 days, and at a 50-percent discount thereafter.
Bloksberg said that the company has not yet determined the pricing structure for single-seat licenses, but they will be available after the software is on the market for a year.
Bernadette Toner ([email protected])