title: An analysis of the validity and utility of the proximon proposition.
abstract: The utilization of metagenomic functional interactions represents a key technique for metagenomic functional annotation efforts. By definition, metagenomic operons represent such interactions, but many operon predictions protocols rely on information about orthology and/or gene function that is frequently unavailable for metagenomic genes. Recently, the concept of the metagenomic proximon was proposed for use in metagenomic scenarios where supplemental information is sparse. In this paper, we examine the validity and utility of the proximon proposition by measuring the extent to which proximons emulate actual operons. Using the Escherichia coli K-12 genome, we compare proximons and operons from the same genome and observe the configurations and cardinalities among their corresponding mappings. The results demonstrate that the vast majority of proximons map discretely to a single operon in a conservative fashion where a typical proximon is synonymous to an equivalent or truncated operon. However, a large proportion of operons had no corresponding mappings to any proximon. Various perspectives of operon and proximon intersection are discussed, along with the potential limitations for proximon detection and usage.
authors.affiliation: Department of Biology, University of Waterloo, 200 University Ave. W., Waterloo, ON, N2L 3G1, Canada. gvey@uwaterloo.ca.
authors.forename: Gregory
authors.identifier: http://orcid.org/0000-0003-1574-1373
authors.initials: G
authors.lastname: Vey
authors.affiliation: Department of Biology, University of Waterloo, 200 University Ave. W., Waterloo, ON, N2L 3G1, Canada.
authors.forename: Trevor C
authors.initials: TC
authors.lastname: Charles
mesh_terms: D000465:Algorithms; D002874:Chromosome Mapping; D048168:Escherichia coli K12 / Q000235:genetics*; D016680:Genome, Bacterial; D056186:Metagenomics; D008957:Models, Genetic; D009876:Operon; D012984:Software
keywords: Functional interaction; Functional metagenomics; Operon; Proximon
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