Predicting Functional Interactions Among Genes in Prokaryotes by Genomic Context

Genomic context methods for finding functions of unannotated genes were implemented very early after the publication of the first few prokaryotic genomes. The ideas behind these methods include gene fusions, conservation of gene adjacency, and the patters of co-occurrence of genes across available genomes. A later addition was the prediction of features related to functional organization, such as operons, stretches of genes co-transcribed into a single messenger RNA. The ideas behind these methods tend to be easy to understand, while the strategies for transforming those basic ideas into predictions can vary in complexity, mostly because genes whose products are known to functionally interact vary in the way they relate to those basic ideas. We present here a view of genomic context methods for predicting functional interactions, with simple examples of their implementation as compared and evaluated using genes whose products are known to functionally interact.