Genome context

III. Gene and Function Prediction by Conservation of Genomic Context. 357... 

The first section of the chapter quantifies the rates at which the various aspects of genomes and the genomic context of any gene evolve. The second section shows how the conservation of genomic context can be used to predict genes, their function, and their functional relations with other genes. The last section shows how the variation of genomic context can indicate a different role of proteins in the cell and the evolution of pathways. 

STRING string.embl.de No restriction PPIs derived from genomic context analysis, experiments, coexpression and literature-based (cover 179 species) von Mering et al. (2005)... 

Huynen, M., Snel, B., Lathe, W. 3rd and Bork, P. (2000) Predicting protein function by genomic context quantitative evaluation and qualitative inferences. Genome Res. 10, 1204—1210. 

The following sections briefly discuss some results and trends in using structure prediction for remote homology detection especially in the genomic context, to aid the structural genomics projects, to further whole genome annotation and to exploit the sequence-to-structure-to-function paradigm for functional predictions. 

Key Words Comparative genomics genome annotation Bidirectional Best Hit (BBH) sequence clustering protein domain genome context. 

Doerks, T., von Mering, C., and Bork, P. (2004) Functional clues for hypothetical proteins based on genomic context analysis in prokaryotes. Nucl. Acids Res. 32, 6321-6326. 

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