Literature DB >> 15706531

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 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 technology back to a full circle.

Mesh:

Year:  2003        PMID: 15706531

Source DB:  PubMed          Journal:  Genome Inform        ISSN: 0919-9454


  15 in total

1.  Genome-wide synteny through highly sensitive sequence alignment: Satsuma.

Authors:  Manfred G Grabherr; Pamela Russell; Miriah Meyer; Evan Mauceli; Jessica Alföldi; Federica Di Palma; Kerstin Lindblad-Toh
Journal:  Bioinformatics       Date:  2010-03-05       Impact factor: 6.937

2.  RazerS--fast read mapping with sensitivity control.

Authors:  David Weese; Anne-Katrin Emde; Tobias Rausch; Andreas Döring; Knut Reinert
Journal:  Genome Res       Date:  2009-07-10       Impact factor: 9.043

3.  Sequence Comparison Without Alignment: The SpaM Approaches.

Authors:  Burkhard Morgenstern
Journal:  Methods Mol Biol       Date:  2021

4.  SwiftOrtho: A fast, memory-efficient, multiple genome orthology classifier.

Authors:  Xiao Hu; Iddo Friedberg
Journal:  Gigascience       Date:  2019-10-01       Impact factor: 6.524

5.  Discriminating antigen and non-antigen using proteome dissimilarity: bacterial antigens.

Authors:  Kamna Ramakrishnan; Darren R Flower
Journal:  Bioinformation       Date:  2010-04-30

6.  Fast alignment-free sequence comparison using spaced-word frequencies.

Authors:  Chris-Andre Leimeister; Marcus Boden; Sebastian Horwege; Sebastian Lindner; Burkhard Morgenstern
Journal:  Bioinformatics       Date:  2014-04-03       Impact factor: 6.937

7.  Lossless filter for multiple repeats with bounded edit distance.

Authors:  Pierre Peterlongo; Gustavo Akio Tominaga Sacomoto; Alair Pereira do Lago; Nadia Pisanti; Marie-France Sagot
Journal:  Algorithms Mol Biol       Date:  2009-01-30       Impact factor: 1.405

8.  Comparative genomic characterization of Francisella tularensis strains belonging to low and high virulence subspecies.

Authors:  Mia D Champion; Qiandong Zeng; Eli B Nix; Francis E Nano; Paul Keim; Chinnappa D Kodira; Mark Borowsky; Sarah Young; Michael Koehrsen; Reinhard Engels; Matthew Pearson; Clint Howarth; Lisa Larson; Jared White; Lucia Alvarado; Mats Forsman; Scott W Bearden; Anders Sjöstedt; Richard Titball; Stephen L Michell; Bruce Birren; James Galagan
Journal:  PLoS Pathog       Date:  2009-05-29       Impact factor: 6.823

9.  Short read DNA fragment anchoring algorithm.

Authors:  Wendi Wang; Peiheng Zhang; Xinchun Liu
Journal:  BMC Bioinformatics       Date:  2009-01-30       Impact factor: 3.169

10.  SeqAn an efficient, generic C++ library for sequence analysis.

Authors:  Andreas Döring; David Weese; Tobias Rausch; Knut Reinert
Journal:  BMC Bioinformatics       Date:  2008-01-09       Impact factor: 3.169

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