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BIBE
2006
IEEE
119views Bioinformatics» more  BIBE 2006»
13 years 11 months ago
Large Grain Size Stochastic Optimization Alignment
DNA sequence alignment is a critical step in identifying homology between organisms. The most widely used alignment program, ClustalW, is known to suffer from the local minima pro...
Perry Ridge, Hyrum Carroll, Dan Sneddon, Mark J. C...
BMCBI
2006
100views more  BMCBI 2006»
13 years 5 months ago
Using the nucleotide substitution rate matrix to detect horizontal gene transfer
Background: Horizontal gene transfer (HGT) has allowed bacteria to evolve many new capabilities. Because transferred genes perform many medically important functions, such as conf...
Micah Hamady, M. D. Betterton, Rob Knight
BMCBI
2008
139views more  BMCBI 2008»
13 years 5 months ago
A topological transformation in evolutionary tree search methods based on maximum likelihood combining p-ECR and neighbor joinin
Background: Inference of evolutionary trees using the maximum likelihood principle is NP-hard. Therefore, all practical methods rely on heuristics. The topological transformations...
Maozu Guo, Jian-Fu Li, Yang Liu
BMCBI
2005
132views more  BMCBI 2005»
13 years 5 months ago
Kalign - an accurate and fast multiple sequence alignment algorithm
Background: The alignment of multiple protein sequences is a fundamental step in the analysis of biological data. It has traditionally been applied to analyzing protein families f...
Timo Lassmann, Erik L. L. Sonnhammer
ISCAPDCS
2007
13 years 7 months ago
Architectural requirements of parallel computational biology applications with explicit instruction level parallelism
—The tremendous growth in the information culture, efficient digital searches are needed to extract and identify information from huge data. The notion that evolution in silicon ...
Naeem Zafar Azeemi