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IJPP
2011
107views more  IJPP 2011»
13 years 2 months ago
Parallel Iterator for Parallelizing Object-Oriented Applications
With the advent of multi-core processors, desktop application developers must finally face parallel computing and its challenges. A large portion of the computational load in a p...
Nasser Giacaman, Oliver Sinnen
RECOMB
2001
Springer
14 years 8 months ago
A new approach to sequence comparison: normalized sequence alignment
The Smith-Waterman algorithm for local sequence alignment is one of the most important techniques in computational molecular biology. This ingenious dynamic programming approach w...
Abdullah N. Arslan, Ömer Egecioglu, Pavel A. ...
COCOA
2007
Springer
14 years 1 months ago
A Lagrangian Relaxation Approach for the Multiple Sequence Alignment Problem
Abstract. We present a branch-and-bound (bb) algorithm for the multiple sequence alignment problem (MSA), one of the most important problems in computational biology. The upper bou...
Ernst Althaus, Stefan Canzar
BCB
2010
156views Bioinformatics» more  BCB 2010»
13 years 2 months ago
Accelerating HMMER on GPUs by implementing hybrid data and task parallelism
Many biologically motivated problems are expressed as dynamic programming recurrences and are difficult to parallelize due to the intrinsic data dependencies in their algorithms. ...
Narayan Ganesan, Roger D. Chamberlain, Jeremy Buhl...
ISMB
1996
13 years 9 months ago
Compact Encoding Strategies for DNA Sequence Similarity Search
Determining whether two DNA sequences are similar is an essential component of DNA sequence analysis. Dynamic programming is the algorithm of choice if computational time is not t...
David J. States, Pankaj Agarwal