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BMCBI
2007
233views more  BMCBI 2007»
14 years 12 months ago
160-fold acceleration of the Smith-Waterman algorithm using a field programmable gate array (FPGA)
Background: To infer homology and subsequently gene function, the Smith-Waterman (SW) algorithm is used to find the optimal local alignment between two sequences. When searching s...
Isaac T. S. Li, Warren Shum, Kevin Truong
BMCBI
2008
109views more  BMCBI 2008»
14 years 12 months ago
ConStruct: Improved construction of RNA consensus structures
Background: Aligning homologous non-coding RNAs (ncRNAs) correctly in terms of sequence and structure is an unresolved problem, due to both mathematical complexity and imperfect s...
Andreas Wilm, Kornelia Linnenbrink, Gerhard Steger
BMCBI
2008
152views more  BMCBI 2008»
14 years 12 months ago
Predicting biological system objectives de novo from internal state measurements
Background: Optimization theory has been applied to complex biological systems to interrogate network properties and develop and refine metabolic engineering strategies. For examp...
Erwin P. Gianchandani, Matthew A. Oberhardt, Antho...
BMCBI
2005
113views more  BMCBI 2005»
14 years 11 months ago
PentaPlot: A software tool for the illustration of genome mosaicism
Background: Dekapentagonal maps depict the phylogenetic relationships of five genomes in a visually appealing diagram and can be viewed as an alternative to a single evolutionary ...
Lutz Hamel, Olga Zhaxybayeva, J. Peter Gogarten
PAMI
2007
159views more  PAMI 2007»
14 years 11 months ago
Soft Color Segmentation and Its Applications
—We propose an automatic approach to soft color segmentation, which produces soft color segments with an appropriate amount of overlapping and transparency essential to synthesiz...
Yu-Wing Tai, Jiaya Jia, Chi-Keung Tang