An automated system for evaluation of the potential functionome: MAPLE version 2.1.0
| Autor: | Wataru Arai, Susumu Goto, Takeaki Taniguchi, Kazuhiro Takemoto, Hideto Takami, Yuki Moriya |
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| Jazyk: | angličtina |
| Rok vydání: | 2016 |
| Předmět: |
0301 basic medicine
Maple Global ocean sampling MAPLE 030106 microbiology General Medicine Computational biology metabolic pathway engineering.material Biology Full Papers Bioinformatics Genome metagenome 03 medical and health sciences 030104 developmental biology Metagenomics Functional module Genetics engineering global ocean sampling (GOS) KEGG Molecular Biology |
| Zdroj: | DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes |
| ISSN: | 1756-1663 1340-2838 |
| Popis: | Metabolic and physiological potential evaluator (MAPLE) is an automatic system that can perform a series of steps used in the evaluation of potential comprehensive functions (functionome) harboured in the genome and metagenome. MAPLE first assigns KEGG Orthology (KO) to the query gene, maps the KO-assigned genes to the Kyoto Encyclopedia of Genes and Genomes (KEGG) functional modules, and then calculates the module completion ratio (MCR) of each functional module to characterize the potential functionome in the user’s own genomic and metagenomic data. In this study, we added two more useful functions to calculate module abundance and Q-value, which indicate the functional abundance and statistical significance of the MCR results, respectively, to the new version of MAPLE for more detailed comparative genomic and metagenomic analyses. Consequently, MAPLE version 2.1.0 reported significant differences in the potential functionome, functional abundance, and diversity of contributors to each function among four metagenomic datasets generated by the global ocean sampling expedition, one of the most popular environmental samples to use with this system. MAPLE version 2.1.0 is now available through the web interface (http://www.genome.jp/tools/maple/) 17 June 2016, date last accessed. |
| Databáze: | OpenAIRE |
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