PatternHunter
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 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.
Keywords for this software
References in zbMATH (referenced in 36 articles , 1 standard article )
Showing results 1 to 20 of 36.
Sorted by year (- Martin, Donald E. K.: Distributions of pattern statistics in sparse Markov models (2020)
- Gagie, Travis; Manzini, Giovanni; Valenzuela, Daniel: Compressed spaced suffix arrays (2017)
- Girotto, Samuele; Comin, Matteo; Pizzi, Cinzia: Fast spaced seed hashing (2017)
- Girotto, Samuele; Comin, Matteo; Pizzi, Cinzia: Metagenomic reads binning with spaced seeds (2017)
- Keith, Jonathan M. (ed.): Bioinformatics. Volume I. Data, sequence analysis, and evolution (2017)
- Liu, Yongchao; Schmidt, Bertil: CUSHAW suite: parallel and efficient algorithms for NGS read alignment (2017)
- Martin, Donald E. K.; Noé, Laurent: Faster exact distributions of pattern statistics through sequential elimination of states (2017)
- Shen, Carol; Shen, Tony; Lin, Jimmy: Comparative assessment of alignment algorithms for NGS data: features, considerations, implementations, and future (2017)
- Vroland, Christophe; Salson, Mikaël; Bini, Sébastien; Touzet, Hélène: Approximate search of short patterns with high error rates using the (01^\ast0) lossless seeds (2016)
- Egidi, Lavinia; Manzini, Giovanni: Design and analysis of periodic multiple seeds (2014)
- Egidi, Lavinia; Manzini, Giovanni: Better spaced seeds using quadratic residues (2013)
- Ji, Zhen; Zhou, Jiarui; Zhu, Zexuan; Chen, Siping: Self-configuration single particle optimizer for DNA sequence compression (2013) ioport
- Elloumi, Mourad (ed.); Zomaya, Albert Y. (ed.): Algorithms in computational molecular biology. Techniques approaches and applications. (2011)
- Blanchet-Sadri, F.; Fowler, Justin; Gafni, Joshua D.; Wilson, Kevin H.: Combinatorics on partial word correlations (2010)
- Chung, Won-Hyoung; Park, Seong-Bae: Hit integration for identifying optimal spaced seeds (2010) ioport
- Jeong, In-Seon; Park, Kyoung-Wook; Kang, Seung-Ho; Lim, Hyeong-Seok: An efficient similarity search based on indexing in large DNA databases (2010)
- Nakato, Ryuichiro; Gotoh, Osamu: Cgaln: fast and space-efficient whole-genome alignment (2010) ioport
- Noé, Laurent; Gîrdea, Marta; Kucherov, Gregory: Designing efficient spaced seeds for SOLiD read mapping (2010)
- Battaglia, Giovanni; Cangelosi, Davide; Grossi, Roberto; Pisanti, Nadia: Masking patterns in sequences: A new class of motif discovery with don’t cares (2009)
- Homer, Nils; Merriman, Barry; Nelson, Stanley F.: Local alignment of two-base encoded DNA sequence (2009) ioport