The Genomics of Restriction and Modification
Roberts, Richard J.
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The discovery of new restriction enzymes has progressed from the slow and laborious process of examining individual bacterial strains experimentally to the much higher through-put that can be obtained using bioinformatics to analyze genome sequences. Nevertheless, both the traditional biochemical approach and the use of biochemistry to test bioinformatics predictions are an integral part of current practices. The analysis of bacterial genomes for their content of genes related to restriction-modification systems faces many of the challenges found more generally when annotating genomes. The methodology that we have developed will be described and examples will be drawn from the analysis of both individual microorganisms and the environmental projects that broadly sample various environments. In the final part of the talk, the more general problem of genome annotation will be discussed and a new project, COMBREX, that aims to accelerate the experimental assignment of function to genes will be described.