The DOI matches its Crossref record; 12 of the 12 references it cites were found in a registry or an index.
PatternHunter: faster and more sensitive homology search
Abstract
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
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Fast and accurate short read alignment with Burrows-Wheeler transform
Li, H., & Durbin, R. (2009) · Bioinformatics · doi:10.1093/bioinformatics/btp324 · Cited by 58,607
Ultrafast and memory-efficient alignment of short DNA sequences to the human genome.
Langmead, B., Trapnell, C., Pop, M., & Salzberg, S. L. (2009) · Genome Biology · doi:10.1186/gb-2009-10-3-r25 · Cited by 21,849
Fast and sensitive protein alignment using DIAMOND
Buchfink, B., Xie, C., & Huson, D. H. (2015) · Nature Methods · doi:10.1038/nmeth.3176 · Cited by 14,201
Fast and accurate long-read alignment with Burrows-Wheeler transform.
Li, H., & Durbin, R. (2010) · Bioinformatics · doi:10.1093/bioinformatics/btp698 · Cited by 12,063
Database resources of the National Center for Biotechnology Information: update
Wheeler, D. L. (2004) · Nucleic Acids Research · doi:10.1093/nar/gkh073 · Cited by 10,641
Metadata
- Authors
- Ma, B., Tromp, J., & Li, M.
- Venue
- Bioinformatics
- Publisher
- Oxford University Press (OUP)
- Published
- 2002-03-01
- Volume
- 18
- Issue
- 3
- Pages
- 440-445
- ISSN
- 1367-4803 (ISSN-L)
- 1367-4811
- OpenAlex
- W2128591967
- Cited by
- 829
- References
- 12
- FWCI
- 14.79
- Type
- journal article
- Language
- en
- Open access
- closed
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