Citation Context

...tion networks are the canonical data sets of the post-genomic era, and more than a dozen methods to detect protein-DNA and protein-protein interactions on a genomic scale have been recently described =-=[1, 2, 3, 4,5, 6, 7, 8, 9]-=-. As many of these methods require no further experimental data beyond a genome sequence, we now have a situation in which a number of different interaction networks are available for each sequenced o...

Citation Context

... algorithm is arguably the most powerful and useful tool in bioinformatics, and has been used to functionally annotate millions of genes saving untold hours of experimentation and providing remarkable insight into biological systems. Although this algorithm is both deceptively simple and remarkably powerful, researchers have recognized that the BLAST algorithm cannot reliably distinguish between orthologous (sequences related through common ancestry) and paralogous (sequence similarity due to an ancestral duplication event) genes [Barbazuk et al., 2000; Chiu et al., 2006; Daubin et al., 2002; Srinivasan et al., 2005]. Determination of orthology or paralogy is critically important because paralogous genes often have distinct functional roles in organisms (e.g., ompF , ompC ). Phylogenetic analyses, on the other hand, easily distinguish orthologs from paralogs given sufficient sampling of related sequences, and these methods have often been used to characterize new functional groups of proteins [Barbazuk et al., 2000; Kelley and Thackray, 1999; Yi et al., 1999]. Given the utility of phylogenetic analyses for classifying orthologs and paralogs, we set forth to determine the effectiveness of newly developed ...

Citation Context

...n map was constructed by retaining the top 50 nonredundant correlates for each gene in the genome (Fig. 1b, inset). Similarly, genome sequence data was used to construct phylogenomic interaction maps =-=(20)-=-, which predict functional interactions based on the principle of coinheritance; genes which are consistently coinherited across evolutionary lines are considered likely to be functionally linked. Usi...

Citation Context

...orks are inferred through indirect correlations, including coexpression under the same conditions [8], in the same tissues [33], or at the same time points [34, 35]; coinheritance in the same species =-=[36, 37]-=-; collocation on chromosomes [38]; coevolution of residues [39] or shared mutant phenotype [40]. These indirect networks are constructed by using variation along one dimension (time, space, environmen...

Citation Context

...then combining these results with measured or predicted structural data. To test this approach, we will make use data from multiple eukaryotes and more than 200 bacterial species described in [7] and =-=[13]-=- to identify proteins and functional modules that remain together across speciation events through evolutionary time. 5s6 Acknowledgments The authors would like to acknowledge Joshua Griffin for his d...

Citation Context

...tome ‘training sets’ to improve predictionss(Munch & Krogh, 2006). EST and digital gene expression data remain resources for novel genesdiscovery (Nesbitt et al., 2010), functional genome annotation (=-=Srinivasan et al., 2005-=-), and forscomparative genomics (Mitreva et al., 2004). Herein, EST data sets for head and body lice weresgenerated by next generation sequencing (NGS). Transcript data were used to (1) validate absin...