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» Differential Scoring for Systolic Sequence Alignment
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BIBE
2007
IEEE
150views Bioinformatics» more  BIBE 2007»
13 years 11 months ago
Differential Scoring for Systolic Sequence Alignment
Systolic implementations of dynamic programming solutions that utilize a similarity matrix can achieve appreciable performance with both course- and fine-grain parallelization. A ...
Antonio E. de la Serna
BMCBI
2006
120views more  BMCBI 2006»
13 years 4 months ago
Optimizing amino acid substitution matrices with a local alignment kernel
Background: Detecting remote homologies by direct comparison of protein sequences remains a challenging task. We had previously developed a similarity score between sequences, cal...
Hiroto Saigo, Jean-Philippe Vert, Tatsuya Akutsu
FPL
2010
Springer
188views Hardware» more  FPL 2010»
13 years 2 months ago
SeqHive: A Reconfigurable Computer Cluster for Genome Re-sequencing
We demonstrate how Field Programmable Gate Arrays (FPGAs) may be used to address the computing challenges associated with assembling genome sequences from recent ultra-high-through...
Kristian Stevens, Henry Chen, Terry Filiba, Peter ...