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DSD
2008
IEEE
107views Hardware» more  DSD 2008»
9 years 5 months ago
Acceleration of Smith-Waterman using Recursive Variable Expansion
Zubair Nawaz, Zaid Al-Ars, Koen Bertels, Mudassir ...
IPPS
2010
IEEE
8 years 9 months ago
Fast Smith-Waterman hardware implementation
The Smith-Waterman (SW) algorithm is one of the widely used algorithms for sequence alignment in computational biology. With the growing size of the sequence database, there is alw...
Zubair Nawaz, Koen Bertels, Huseyin Ekin Sumbul
SAMOS
2015
Springer
3 years 7 months ago
An FPGA-based systolic array to accelerate the BWA-MEM genomic mapping algorithm
—We present the first accelerated implementation of BWA-MEM, a popular genome sequence alignment algorithm widely used in next generation sequencing genomics pipelines. The Smit...
Ernst Joachim Houtgast, Vlad Mihai Sima, Koen Bert...
IPPS
2009
IEEE
9 years 6 months ago
Flexible pipelining design for recursive variable expansion
Many image and signal processing kernels can be optimized for performance consuming a reasonable area by doing loops parallelization with extensive use of pipelining. This paper p...
Zubair Nawaz, Thomas Marconi, Koen Bertels, Todor ...
STTT
2008
95views more  STTT 2008»
8 years 11 months ago
FAST: acceleration from theory to practice
Abstract. Fast is a tool for the analysis of systems manipulating unbounded integer variables. We check safety properties by computing the reachability set of the system under stud...
Sébastien Bardin, Alain Finkel, Jér&...
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