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BMCBI
2008
211views more  BMCBI 2008»
13 years 5 months ago
CUDA compatible GPU cards as efficient hardware accelerators for Smith-Waterman sequence alignment
Background: Searching for similarities in protein and DNA databases has become a routine procedure in Molecular Biology. The Smith-Waterman algorithm has been available for more t...
Svetlin Manavski, Giorgio Valle
IPPS
2009
IEEE
13 years 11 months ago
Parallel reconstruction of neighbor-joining trees for large multiple sequence alignments using CUDA
Computing large multiple protein sequence alignments using progressive alignment tools such as ClustalW requires several hours on state-of-the-art workstations. ClustalW uses a th...
Yongchao Liu, Bertil Schmidt, Douglas L. Maskell
IPPS
2009
IEEE
13 years 11 months ago
Accelerating error correction in high-throughput short-read DNA sequencing data with CUDA
Emerging DNA sequencing technologies open up exciting new opportunities for genome sequencing by generating read data with a massive throughput. However, produced reads are signif...
Haixiang Shi, Bertil Schmidt, Weiguo Liu, Wolfgang...
TC
2010
13 years 3 months ago
Network-on-Chip Hardware Accelerators for Biological Sequence Alignment
—The most pervasive compute operation carried out in almost all bioinformatics applications is pairwise sequence homology detection (or sequence alignment). Due to exponentially ...
Souradip Sarkar, Gaurav Ramesh Kulkarni, Partha Pr...