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Literature DB >> 15359419

Patternhunter II: highly sensitive and fast homology search.

Ming Li¹, Bin Ma, Derek Kisman, John Tromp.

Abstract

Extending the single optimized spaced seed of PatternHunter(20) to multiple ones, PatternHunter II simultaneously remedies the lack of sensitivity of Blastn and the lack of speed of Smith-Waterman, for homology search. At Blastn speed, PatternHunter II approaches Smith-Waterman sensitivity, bringing homology search methodology research back to a full circle.

Mesh：

Year: 2004 PMID： 15359419 DOI： 10.1142/s0219720004000661

Source DB: PubMed Journal: J Bioinform Comput Biol ISSN： 0219-7200 Impact factor: 1.122

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Cited

41 in total

1. A unifying framework for seed sensitivity and its application to subset seeds.

Authors: Gregory Kucherov; Laurent Noé; Mikhail Roytberg
Journal: J Bioinform Comput Biol Date: 2006-04 Impact factor: 1.122

2. ZOOM! Zillions of oligos mapped.

Authors: Hao Lin; Zefeng Zhang; Michael Q Zhang; Bin Ma; Ming Li
Journal: Bioinformatics Date: 2008-08-06 Impact factor: 6.937

3. Biosequence Similarity Search on the Mercury System.

Authors: Praveen Krishnamurthy; Jeremy Buhler; Roger Chamberlain; Mark Franklin; Kwame Gyang; Arpith Jacob; Joseph Lancaster
Journal: J VLSI Signal Process Syst Signal Image Video Technol Date: 2007

4. Systematic discovery of regulatory motifs in Fusarium graminearum by comparing four Fusarium genomes.

Authors: Lokesh Kumar; Andrew Breakspear; Corby Kistler; Li-Jun Ma; Xiaohui Xie
Journal: BMC Genomics Date: 2010-03-26 Impact factor: 3.969

5. A coverage criterion for spaced seeds and its applications to support vector machine string kernels and k-mer distances.

Authors: Laurent Noé; Donald E K Martin
Journal: J Comput Biol Date: 2014-12 Impact factor: 1.479

Patternhunter II: highly sensitive and fast homology search.

1. A unifying framework for seed sensitivity and its application to subset seeds.

2. ZOOM! Zillions of oligos mapped.

3. Biosequence Similarity Search on the Mercury System.

4. Systematic discovery of regulatory motifs in Fusarium graminearum by comparing four Fusarium genomes.

5. A coverage criterion for spaced seeds and its applications to support vector machine string kernels and k-mer distances.

6. Short Read Mapping: An Algorithmic Tour.

7. Optimal neighborhood indexing for protein similarity search.

8. Cgaln: fast and space-efficient whole-genome alignment.

9. BOND: Basic OligoNucleotide Design.

10. PerM: efficient mapping of short sequencing reads with periodic full sensitive spaced seeds.