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PatternHunter

PatternHunter is a commercially available homology search instrument software that uses sequence alignment techniques. It was initially developed in… 
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BLASTFASTAList of sequence alignment softwareMUMmer

Broader (1)

Bioinformatics

Papers overview

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Review
2016
Review
2016
From BLAST to PatternHunter: the Development of Alignment Tools and Genomic Research
Developed in 1990, BLAST remained a most widely used heuristic in homology search. Its concept and algorithm of using seed… 
2015
2015
An improvement of the overlap complexity in the spaced seed searching problem between genomic DNAs
In homology search, finding optimal multiple spaced seeds in genomic DNA sequences is NP-hard but even finding good ones is very… 
2013
2013
RAIDER: Rapid Ab Initio Detection of Elementary Repeats
Here we present RAIDER, a tool for the de novo identification of elementary repeats. The problem of searching for genomic repeats… 
2010
2010
A generalized sequence pattern matching algorithm using complementary dual-seeding
In this work, we define generalized (sequence) patterns, which is based on several real Biological problems, including… 
2009
2009
Spaced Seeds Design Using Perfect Rulers ?
We consider the problem of lossless spaced seed design for approximate pattern matching. We show that, using mathematical objects… 
2008
2008
Accelerating Data-Serial Applications on Data-Parallel GPGPUs: A Systems Approach
The general-purpose graphics processing unit (GPGPU) continues to make significant strides in high-end computing by delivering… 
2008
2008
YASS : Recherche de similaritées dans les séquences d ’ ADN
We describe YASS – a new tool for finding local similarities in DNA sequences. The YASS algorithm first scans the sequence(s) and… 
2008
2008
Computing Alignment Seed Sensitivity with Probabilistic Arithmetic Automata
Heuristic sequence alignment and database search algorithms, such as PatternHunter and BLAST, are based on the initial discovery… 
2006
2006
Index Structures in Biological Sequence Analysis: From Simplicity to Complexity and Back
72 boolean, 28 byte, 28 case, 3 5 catch, 9 8 char, 28 class, 21 default, 3 5 double, 21 , 28 do, 3 1 else, 3 2 extends, 23 , 6 6… 
2004
2004
Sensibilite de graines espacees de type subset seed
Les heuristiques d’alignement local à base de graines espacées (BLASTZ [6], PatternHunter [4, 3], YASS [5]) dépendent très… 
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