Gene sequencing on the Virtex-5

And now for something completely different: According to the online genome-sequencing news site, Sequence, Stone Ridge Technology Inc. of Bel Air, MD has been awarded $150,000 from the National Science Foundation for a 2010 study of using reconfigurability in a bioinformatics test to perform first-stage alignment and mapping in gene-sequencing studies. Stone Ridge believes that by implementing an open-source dedicated algorithm on dual FPGAs, a PCI Express board would be able to perform first-stage sequencing 50 to 100 times faster than hardware based on a standard integer CPU.

While Stone Ridge has not indicated how closely the special-purpose platform will resemble its standard reconfigurable single-board computer, the company’s RDX-11 is based on a PCI Express card with three Virtex-5 FPGAs. The decision to seek grants in vertical markets such as molecular biology is a smart one. The last decade of start-and-stop experiments with reconfigurable platforms shows that users are still a little uncertain as to how to optimize reconfigurable hardware. But if hardware developers use a common, FPGA-based platform to develop a number of single-purpose vertical single-board computers, reconfigurability will gain popularity through indirect means. Kudos to Stone Ridge, and we would not be surprised to find other small companies follow this route.