Fri, Mar 19, 2004: BSI Releases Complete Homology Suite PatternHunter 2.0
Bioinformatics Solutions Inc., an advanced bioinformatics software provider is excited to announce that the novel homology search tool, PatternHunter 2.0 is now available as a complete suite.
PatternHunter 2.0 is a general-purpose homology search tool used by leading genomic centers worldwide. It now has the full functionalities of BLAST (BLASTn, BLASTp, tBLASTx, tBLAST, BLASTx) and input and output formats compatible with BLAST. With BSI's proprietary multiple optimal spaced seed technology and algorithms that are well recognized in the research community "Bioinformatics, 18(3):440-445. March 2002", PatternHunter is much more sensitive and many times faster than BLAST. Says President Ming Li, 搃n the 1980抯, BLAST was designed to speed up the Smith-Waterman algorithm for homology search by trading sensitivity for speed. Today, BLAST and Smith-Waterman are no longer sufficient for the exponential growth of genomics data. PatternHunter 2.0 finally has achieved two goals in one program at the same time.? PatternHunter 2.0 is speed and sensitivity without compromise.PatternHunter 2.0 uses modern homology search technology ?i.e. optimized multiple spaced seeds. Says Li, The program changes the way homology search is done. No longer do researchers need to trade sensitivity for speed. PatternHunter can approach Smith-Waterman sensitivity and yet run 3000 times faster.?Please see our "PatternHunter II paper", to find out how we have done it.
There are many new features in the complete suite. PatternHunter 2.0 does gapped alignments, while tBLASTx cannot. PatternHunter new algorithm explicitly avoids 6 frame translations, allowing frame shift gaps. PatternHunter 2.0 can now search against arbitrarily large databases without running out of memory. PatternHunter 2.0 is a complete solution, replacing MegaBlast for highly similar sequences, MUMmer for very similar genomes, and specialized programs to search for SNPs. MegaBlast achieves its speed by longer seeds and MUMmer uses suffix trees, which are not suitable for approximate pattern matching. Both approaches result in low sensitivity. Without compromising sensitivity, PatternHunter 2.0 gives you faster speed than both. There is no more need to resort to these specialized programs for special purposes, PatternHunter 2.0 does them all: high sensitivity, high quality and high speed, for whatever input. PatternHunter 2.0 not only performs better or faster than BLAST, MegaBlast, MUMmer, or Smith-Waterman dynamic programming, but sometimes it is the only choice. States Li, One of our commercial clients was interested in comparing more than three million 21-mers (short DNA sequences of length 21) against their whole DNA database and allowing 25% mismatches. BLAST did not work because its sensitivity is too low to find these short and distant homologies, so Smith-Waterman was their only alternative. However, at the snail's pace set by Smith-Waterman, it would have taken 10 years to compare the three million 21-mers. Fortunately, that customer found PatternHunter 2.0! By using 40 optimized spaced seeds of weight 9 simultaneously, PatternHunter guaranteed a 100% sensitivity at the required similarity level (25% mismatches in a 21-mer), and finished the job in only 8 days.? PatternHunter 2.0 is not free, but it is a smart alternative because PatternHunter 2.0 saves! The ability to achieve the most accurate results at increased speed, saves you time. Performing the most sensitive homology searches you were unable to perform previously, may enable you to find drug targets that might otherwise have been overlooked, reduce time to market for your products and reduce the need to upgrade costly supercomputing hardware every few years. Whether for large database query, genome-genome comparison or DNA-protein translated search, BSI has the solution: PatternHunter 2.0. For an evaluation, visit our website at "Bioinformaticssolutions.com" or send an email to ph-sales@bioinformaticssolutions.com. Bioinformatics Solutions (BSI) provides solutions to core bioinformatics problems in the pharmaceutical and biotech industry, by innovative ideas, advanced algorithms and top-notch software development. In addition to PatternHunter software, BSI offers other products like, RAPTOR and PROSPECT PRO, 3-D protein structure prediction software and PEAKS, for de novo and protein identification of ms/ms data. BSI is headquartered in Waterloo, Ontario. Contact us at (519) 885-8288, ext. 10.
