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» A Comparison of RESTART Implementations
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ISHPC
2003
Springer
15 years 3 months ago
Performance Study of a Whole Genome Comparison Tool on a Hyper-Threading Multiprocessor
We developed a multithreaded parallel implementation of a sequence alignment algorithm that is able to align whole genomes with reliable output and reasonable cost. This paper pres...
Juan del Cuvillo, Xinmin Tian, Guang R. Gao, Milin...
BMCBI
2008
95views more  BMCBI 2008»
14 years 10 months ago
Universal seeds for cDNA-to-genome comparison
Background: To meet the needs of gene annotation for newly sequenced organisms, optimized spaced seeds can be implemented into cross-species sequence alignment programs to accurat...
Leming Zhou, Jonathan Stanton, Liliana Florea
WISTP
2010
Springer
15 years 4 months ago
Towards Electrical, Integrated Implementations of SIMPL Systems
ct This paper discusses the practical implementation of a novel security tool termed SIMPL system, which was introduced in [1]. SIMPL systems can be regarded as a public key versio...
Ulrich Rührmair, Qingqing Chen, Martin Stutzm...
FCCM
2009
IEEE
169views VLSI» more  FCCM 2009»
15 years 4 months ago
RC-BLASTn: Implementation and Evaluation of the BLASTn Scan Function
BLASTn is a tool universally used by biologists to identify similarities between nucleotide based biological genome sequences. This report describes an FPGA based hardware impleme...
Siddhartha Datta, Parag Beeraka, Ron Sass
ISHPC
1997
Springer
15 years 1 months ago
Implementing Iterative Solvers for Irregular Sparse Matrix Problems in High Performance Fortran
Abstract. Writing e cient iterative solvers for irregular, sparse matrices in HPF is hard. The locality in the computations is unclear, and for e ciency we use storage schemes that...
Eric de Sturler, Damian Loher