Synonyms
Functional potential evaluator
Definition
Although one of the main goals of genomic analysis is to elucidate the comprehensive functions (functionome) in individual organisms or a whole community in various environments, a standard evaluation method for discerning the functional potentials harbored within the genome or metagenome has not yet been established. Thus, a new evaluation method for the potential functionome, based on the completion ratio of Kyoto Encyclopedia of Genes and Genomes (KEGG) functional modules, was developed. Basic methodology and application of this method for comparative functional genomics and metagenomics are expounded in this entry.
Introduction
One of the main goals of genomic and metagenomic analyses is to extract the comprehensive functions (functionome) harbored in an individual organism or a whole community in various environments. However, evaluating the potential functionome is still difficult when compared with the functional annotation of...
This is a preview of subscription content, log in via an institution to check access.
References
Eckburg PB, Bik EM, Bernstein CN, et al. Diversity of the human intestinal microbial flora. Science. 2005;308:1635–8.
Huson DH, Mitra S, Ruscheweyh HJ, et al. Integrative analysis of environmental sequences using MEGAN4. Genome Res. 2011;21:1552–60.
Kanehisa M, Goto S. KEGG: kyoto encyclopedia of genes and genomes. Nucleic Acids Res. 2000;28:27–30.
Kanehisa M, Araki M, Goto S, et al. KEGG for linking genomes to life and environment. Nucleic Acids Res. 2008;36:D480–4.
Kurokawa K, Itoh T, Kuwahara T, et al. Comparative metagenomics revealed commonly enriched gene sets in human gut microbiome. DNA Res. 2007;14:169–81.
Li JV, Ashrafian H, Bueter M, et al. Metabolic surgery profoundly influences gut microbial-host metabolic cross-talk. Gut. 2011;60:1214–23.
Markowitz VM, Chen I-MA, Palaniappan K, et al. IMG: the integrated microbial genomes database and comparative analysis system. Nucleic Acids Res. 2012;40:D115–22.
Meyer F, Paarmann D, D’Souza M, et al. The metagenomics RAST server – a public resource for the automatic phylogenetic and functional analysis of metagenomes. BMC Bioinformatics. 2008;9:386.
Moriya Y, Itoh M, Okuda S, et al. KAAS: an automatic genome annotation and pathway reconstruction server. Nucleic Acids Res. 2007;35:W182–5.
Overbeek R, Begley T, Butler RM, et al. The subsystems approach to genome annotation and its use in the project to annotate 1000 genomes. Nucleic Acids Res. 2005;33:5691–702.
Takami H. Genomic diversity of extremophilic Gram-positive endospore-forming Bacillus-related species. In: Williams CR, editor. Trends in genome research. New York: NOVA Publisher; 2006. p. 25–85.
Takami H, Taniguchi T, Moriya Y, et al. Evaluation method for the potential functionome harbored in the genome and metagenome. BMC Genomics. 2012;13:699.
Uchiyama I. Multiple genome alignment for identifying the core structure among moderately related microbial genomes. BMC Genomics. 2008;9:515.
Willke A, Harrison T, Wilkening J, et al. The M5nr: a novel non-redundant database containing protein sequences and annotations from multiple sources and associated tools. BMC Bioinformatics. 2012;13:141.
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2014 Springer Science+Business Media New York
About this entry
Cite this entry
Takami, H. (2014). New Method for Comparative Functional Genomics and Metagenomics Using KEGG MODULE. In: Nelson, K. (eds) Encyclopedia of Metagenomics. Springer, New York, NY. https://doi.org/10.1007/978-1-4614-6418-1_183-3
Download citation
DOI: https://doi.org/10.1007/978-1-4614-6418-1_183-3
Received:
Accepted:
Published:
Publisher Name: Springer, New York, NY
Online ISBN: 978-1-4614-6418-1
eBook Packages: Springer Reference Biomedicine and Life SciencesReference Module Biomedical and Life Sciences