Methods in Molecular Biology™ Volume 453, 2008, pp 181-199

Inferring Functional Relationships from Conservation of Gene Order

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The idea behind the gene neighbor method is that conservation of gene order in evolutionarily distant prokaryotes indicates functional association. The procedure presented here starts with the organization of all the genomes into pairs of adjacent genes. Then, pairs of genes in a genome of interest are mapped to their corresponding orthologs in other, informative, genomes. The final step is to determine whether the orthologs of each original pair of genes are also adjacent in the informative genome.