Titlebook: Bioinformatics Research and Applications; Fourth International Ion Măndoiu,Raj Sunderraman,Alexander Zelikovsky Conference proceedings 2008

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Hierarchical Clustering Using Constraints,f constraints the corresponding part of the supertree is identified and its set of constraints is displayed such as the user may decide to modify or keep it. Our algorithm is not affected by the order in which the input phylogenies or other constraints are presented. We apply our method to a number of data sets.

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Generalized Gene Adjacencies, Graph Bandwidth and Clusters in Yeast Evolution, and to what extent they are preserved from ancestor to descendant in a phylogenetic tree. We infer the latter property by dynamic programming optimization of the presence of individual edges at the ancestral nodes of the phylogeny. We apply our analysis to a set of genomes drawn from the Yeast Gene Order Browser.

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0302-9743 lysis, gene networks, genome analysis, motif finding, pathways, protein structure prediction, protein domain interactions, phylogenetics, and software tools.978-3-540-79449-3978-3-540-79450-9Series ISSN 0302-9743 Series E-ISSN 1611-3349

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Estimating Pairwise Statistical Significance of Protein Local Alignments Using a Clustering-Classififferent cluster pairs has large variability even for the same scoring scheme, underscoring the heavy dependence of . and . on the amino acid composition. The proposed approach in this paper is an attempt to separate the influence of amino acid composition in estimation of statistical significance o

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Gapped Extension for Local Multiple Alignment of Interspersed DNA Repeats,on frequencies for nucleotide substitutions can be derived from any strand/species-symmetric nucleotide substitution matrix, and we have developed a method to adapt an arbitrary substitution matrix (i.e. HOXD) to organisms with different G+C content. We evaluate the performance of our method and pre

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