PatternHunter protocols

PatternHunter specifications


Unique identifier OMICS_03748
Name PatternHunter
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Stability No
Maintained No


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Publication for PatternHunter

PatternHunter IN pipelines

PMCID: 3091654
PMID: 20678236
DOI: 10.1186/1471-2164-11-458

[…] reads are required. surprisingly, megablast with contiguous seeds performs better than discontiguous seed megablast and blastz for alignment of ovine reads to the equine and bovine genomes. patternhunter would perform much better if it were able to effectively utilise soft masking. a range of programs and parameter settings can be quickly surveyed with datasets appropriate […]

PMCID: 2640386
PMID: 19087280
DOI: 10.1186/1471-2105-9-534

[…] [3] and blast [4] and including specific methods for protein similarities such as blastp [5]. seed-based heuristics were recently enhanced by advanced seeding tools like the spaced seeds used in patternhunter [6] or yass [7] (see [8] for a recent survey). authors of this paper also worked on the alliance between advanced seeds techniques and reconfigurable architectures [9]., the main idea […]

PatternHunter institution(s)
Computer Science Department, University of Western Ontario, London, Canada; Bioinformatics Solutions Inc; Waterloo, Ont, Canada

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