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PETRA
2010
ACM
13 years 7 months ago
Benchmarking dynamic time warping for music retrieval
We study the performance of three dynamic programming methods on music retrieval. The methods are designed for time series matching but can be directly applied to retrieval of mus...
Jefrey Lijffijt, Panagiotis Papapetrou, Jaakko Hol...
BMCBI
2002
100views more  BMCBI 2002»
13 years 5 months ago
An algorithm and program for finding sequence specific oligo-nucleotide probes for species identification
Background: The identification of species or species groups with specific oligo-nucleotides as molecular signatures is becoming increasingly popular for bacterial samples. However...
Alexander E. Pozhitkov, Diethard Tautz
BMCBI
2008
103views more  BMCBI 2008»
13 years 5 months ago
TOPS++FATCAT: Fast flexible structural alignment using constraints derived from TOPS+ Strings Model
Background: Protein structure analysis and comparison are major challenges in structural bioinformatics. Despite the existence of many tools and algorithms, very few of them have ...
Mallika Veeramalai, Yuzhen Ye, Adam Godzik
BMCBI
2011
12 years 9 months ago
Faster Smith-Waterman database searches with inter-sequence SIMD parallelisation
Background: The Smith-Waterman algorithm for local sequence alignment is more sensitive than heuristic methods for database searching, but also more time-consuming. The fastest ap...
Torbjørn Rognes
BIBE
2008
IEEE
142views Bioinformatics» more  BIBE 2008»
14 years 7 days ago
Optimizing performance, cost, and sensitivity in pairwise sequence search on a cluster of PlayStations
— The Smith-Waterman algorithm is a dynamic programming method for determining optimal local alignments between nucleotide or protein sequences. However, it suffers from quadrati...
Ashwin M. Aji, Wu-chun Feng