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IPPS
2008
IEEE
15 years 8 months ago
Ordered index seed algorithm for intensive DNA sequence comparison
This paper presents a seed-based algorithm for intensive DNA sequence comparison. The novelty comes from the way seeds are used to efficiently generate small ungapped alignments ...
Dominique Lavenier
IPPS
2005
IEEE
15 years 8 months ago
Comparison of Current BLAST Software on Nucleotide Sequences
The computational power needed for searching exponentially growing databases, such as GenBank, has increased dramatically. Three different implementations of the most widely used ...
I. Elizabeth Cha, Eric C. Rouchka
BMCBI
2008
211views more  BMCBI 2008»
15 years 2 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
115
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IISWC
2006
IEEE
15 years 8 months ago
Performance Analysis of Sequence Alignment Applications
— Recent advances in molecular biology have led to a continued growth in the biological information generated by the scientific community. Additionally, this area has become a m...
Friman Sánchez, Esther Salamí, Alex ...
ICCS
2005
Springer
15 years 7 months ago
Generating Parallel Algorithms for Cluster and Grid Computing
We revisit and use the dependence transformation method to generate parallel algorithms suitable for cluster and grid computing. We illustrate this method in two applications: to o...
Ulisses Kendi Hayashida, Kunio Okuda, Jairo Panett...