Titlebook: Research in Computational Molecular Biology; 10th Annual Internat Alberto Apostolico,Concettina Guerra,Michael Water Conference proceedings

strain

Clustering Near-Identical Sequences for Fast Homology Search,ive . and a set of corresponding edits to that sequence. During search, the query is compared to only the union-sequences representing each cluster; cluster members are then only reconstructed and aligned if the union-sequence achieves a sufficiently high score. Using this approach in BLAST results

Panacea

低能儿

A Probabilistic Model for Gene Content Evolution with Duplication, Loss, and Horizontal Transfer,fer, gene duplication, and gene loss, in addition to branch lengths in the phylogeny. The likelihood for the changes in the size of a gene family across different organisms can be calculated in .(.+. .) time and .(.+. .) space, where . is the number of organisms, . is the height of the phylogeny, an

Accommodation

A Sublinear-Time Randomized Approximation Scheme for the Robinson-Foulds Metric,hm. When faced with the need to compare large numbers of large trees, however, even linear time becomes prohibitive. We present a randomized approximation scheme that provides, with high probability, a (1+.) approximation of the true RF metric for all pairs of trees in a given collection. Our approa

成份

Integrated Protein Interaction Networks for 11 Microbes,of even well studied functional modules. Our work represents the largest collection of probabilistic protein interaction networks compiled to date, and our methods can be applied to any sequenced organism and any kind of experimental or computational technique which produces pairwise measures of protein interaction.

FLAGR

,Hypergraph Model of Multi-residue Interactions in Proteins: Sequentially–Constrained Partitioning Aracterized by the total perturbation to edge weights. We prove this problem to be NP-hard in general, but develop exact and heuristic polynomial-time algorithms for a number of important cases. Application to the beta-lactamase family demonstrates the utility of our algorithms in planning site-directed recombination.

TOXIC

Albinism

An Improved Statistic for Detecting Over-Represented Gene Ontology Annotations in Gene Sets, a biological dataset further supports our method. Our approach comes at no additional computational complexity when compared to the standard approach. An implementation is available within the framework of the freely available Ontologizer application.

CARK

Protein Function Annotation Based on Ortholog Clusters Extracted from Incomplete Genomes Using Comb sequences..We report on a candidate annotation for proteins in the rice genome using ortholog clusters constructed from four partially complete cereal genomes – barley, maize, sorghum, wheat and the complete genome of ..

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