Abstract
A combined genomics and in situ proteomics approach can be used to determine and classify the relatedness of organisms. The common set of proteins shared within a group of genomes is encoded by the “core” set of genes, which is increasingly recognized as a metric for parsing viral and bacterial species. These can be described by the concept of a “pan-genome”, which consists of this “core” set and a “dispensable” set, i.e., genes found in one or more but not all organisms in the grouping. “CoreGenesUniqueGenes” (CGUG) is a web-based tool that determines this core set of proteins in a set of genomes as well as parses the dispensable set of unique proteins in a pair of viral or small bacterial genomes. This proteome-based methodology is validated using bacteriophages, aiding the reevaluation of current classifications of bacteriophages. The utility of CGUG in the analysis of small bacterial genomes and the annotation of hypothetical proteins is also presented.
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Acknowledgments
We thank Drs. Andrew Kropinski and Rob Lavigne for their very helpful suggestions of features to add to CoreGenes. We thank Jason Seto for editorial comments and Chris Ryan for maintaining the server on which the software is hosted. This paper is based on Mahadevan and Seto (BIOCOMP ’09).
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Mahadevan, P., Seto, D. (2010). Taxonomic Parsing of Bacteriophages Using Core Genes and In Silico Proteome-Based CGUG and Applications to Small Bacterial Genomes. In: Arabnia, H. (eds) Advances in Computational Biology. Advances in Experimental Medicine and Biology, vol 680. Springer, New York, NY. https://doi.org/10.1007/978-1-4419-5913-3_43
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DOI: https://doi.org/10.1007/978-1-4419-5913-3_43
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