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BMCBI
2007
233views more  BMCBI 2007»
13 years 10 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
154views more  BMCBI 2008»
13 years 10 months ago
Extension of the COG and arCOG databases by amino acid and nucleotide sequences
Background: The current versions of the COG and arCOG databases, both excellent frameworks for studies in comparative and functional genomics, do not contain the nucleotide sequen...
Florian Meereis, Michael Kaufmann
BMCBI
2008
87views more  BMCBI 2008»
13 years 10 months ago
Volume-based solvation models out-perform area-based models in combined studies of wild-type and mutated protein-protein interfa
Background: Empirical binding models have previously been investigated for the energetics of protein complexation (G models) and for the influence of mutations on complexation (i....
Salim Bougouffa, Jim Warwicker
BMCBI
2008
83views more  BMCBI 2008»
13 years 10 months ago
Models of deletion for visualizing bacterial variation: an application to tuberculosis spoligotypes
Background: Molecular typing methods are commonly used to study genetic relationships among bacterial isolates. Many of these methods have become standardized and produce portable...
Josephine F. Reyes, Andrew R. Francis, Mark M. Tan...
BMCBI
2008
148views more  BMCBI 2008»
13 years 10 months ago
Critical assessment of alignment procedures for LC-MS proteomics and metabolomics measurements
Background: Liquid chromatography coupled to mass spectrometry (LC-MS) has become a prominent tool for the analysis of complex proteomics and metabolomics samples. In many applica...
Eva Lange, Ralf Tautenhahn, Steffen Neumann, Cleme...