PatternHunter: faster and more sensitive homology search
Motivation: Genomics and proteomics studies routinely depend on homology searches based on the strategy of finding short seed matches which are then extended. The exploding genomic data growth presents a dilemma for DNA homology search techniques: increasing seed size decreases sensitivity whereas d...
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| Veröffentlicht in: | Bioinformatics 2002-03, Vol.18 (3), p.440-445 |
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| container_title | Bioinformatics |
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| creator | Ma, Bin Tromp, John Li, Ming |
| description | Motivation: Genomics and proteomics studies routinely depend on homology searches based on the strategy of finding short seed matches which are then extended. The exploding genomic data growth presents a dilemma for DNA homology search techniques: increasing seed size decreases sensitivity whereas decreasing seed size slows down computation. Results: We present a new homology search algorithm ‘PatternHunter’ that uses a novel seed model for increased sensitivity and new hit-processing techniques for significantly increased speed. At Blast levels of sensitivity, PatternHunter is able to find homologies between sequences as large as human chromosomes, in mere hours on a desktop. Availability: PatternHunter is available at http://www.bioinformaticssolutions.com, as a commercial package. It runs on all platforms that support Java. PatternHunter technology is being patented; commercial use requires a license from BSI, while non-commercial use will be free. Contact: mli@cs.ucsb.edu |
| doi_str_mv | 10.1093/bioinformatics/18.3.440 |
| format | Article |
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| source | MEDLINE; Oxford Journals Open Access Collection; EZB-FREE-00999 freely available EZB journals; Alma/SFX Local Collection |
| subjects | Algorithms Base Sequence Biological and medical sciences Databases, Nucleic Acid DNA - genetics Fundamental and applied biological sciences. Psychology General aspects Genome Mathematics in biology. Statistical analysis. Models. Metrology. Data processing in biology (general aspects) Models, Statistical Molecular Sequence Data National Library of Medicine (U.S.) Quality Control Sensitivity and Specificity Sequence Alignment - methods Sequence Alignment - statistics & numerical data Sequence Homology Software Time Factors United States |
| title | PatternHunter: faster and more sensitive homology search |
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