Mon, Nov 26, 2001: BSI Brings Algorithmic Solutions to Range of Bioinformatics Problems
BSI was featured in the November 26th issue of BioInform. For a brief excerpt read below - the full article can be read at the BioInform website. It all about the algorithms, according to Ming Li, CEO of Waterloo, Ontario-based Bioinformatics Solutions. Unlike many bioinformatics companies, who Concentrate on putting a good user interface on free software,Li said his company is focused on Developing proprietary software based on advanced algorithm designs to provide real solutions to bioinformatics problems.? The eight-employee company had its roots in the bioinformatics research group at the University of Waterloo. Armed with around $500,000 in venture capital, BSI launched officially last October with the hire of its first full-time employee. The company newest product, PatternHunter, is a homology search algorithm that is hundreds of times faster than Blast at the same sensitivity, according to Li. While most approaches to speeding up homology searches rely on tweaking or parallelizing the original Blast algorithm, Li and his colleagues started from scratch with their approach. The PatternHunter algorithm, which they describe in an upcoming Bioinformatics article, is based on a novel approach to seeding process of finding short Seed matches which are then extended into longer alignments. While Blast looks for seed groupings of consecutive letters, PatternHunter uses groupings of non-consecutive letters, which increases the algorithm sensitivity, according to BSI. The Mouse Genome Project is currently using PatternHunter to compare the mouse and human genomes, Li said, a process that would take 19 years using Blast. At the same sensitivity, PatternHunter takes 20 days on a single PC.? Li said that BSI is still working on adding protein sequence comparison capability to PatternHunter, a feature that should be available in a few weeks. In addition to PatternHunter, BSI also offers Prospect, a 3-D protein structure prediction program based on threading techniques; Copia, which finds consensus patterns in proteins; and Hyperclean, which computes phylogenies of species. BSI is also partnering with Caprion Pharmaceuticals to develop new algorithms for mass spec analysis.
