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Methods Mol Biol. 2017;1526:41-63.

Inferring Functional Relationships from Conservation of Gene Order.

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Department of Biology, Wilfrid Laurier University, 75 University Ave W, Waterloo, ON, Canada, N2L 3C5.


Predicting functional associations using the Gene Neighbor Method depends on the simple idea that if genes are conserved next to each other in evolutionarily distant prokaryotes they might belong to a polycistronic transcription unit. The procedure presented in this chapter starts with the organization of the genes within genomes into pairs of adjacent genes. Then, the pairs of adjacent genes in a genome of interest are mapped to their corresponding orthologs in other, informative, genomes. The final step is to verify if the mapped orthologs are also pairs of adjacent genes in the informative genomes.


Conservation of gene order; Functional inference; Gene neighbor method; Genomic context; Operon

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