MetaboAnnotator: an efficient toolbox to annotate metabolites in genome-scale metabolic reconstructions.

Autor:	Thiele I; School of Medicine, University of Galway, Galway H91TK33, Ireland.; Ryan Institute, University of Galway, Galway H91TK33, Ireland.; Division of Microbiology, University of Galway, Galway H91TK33, Ireland.; APC Microbiome Ireland, University College Cork, Cork T12K8AF, Ireland., Preciat G; Analytical BioSciences Division, Leiden Academic Centre for Drug Research, Leiden University, 2311 EZ, The Netherlands., Fleming RMT; School of Medicine, University of Galway, Galway H91TK33, Ireland.; Analytical BioSciences Division, Leiden Academic Centre for Drug Research, Leiden University, 2311 EZ, The Netherlands.
Jazyk:	angličtina
Zdroj:	Bioinformatics (Oxford, England) [Bioinformatics] 2022 Oct 14; Vol. 38 (20), pp. 4831-4832.
DOI:	10.1093/bioinformatics/btac596
Abstrakt:	Motivation: Genome-scale metabolic reconstructions have been assembled for thousands of organisms using a wide range of tools. However, metabolite annotations, required to compare and link metabolites between reconstructions, remain incomplete. Here, we aim to further extend metabolite annotation coverage using various databases and chemoinformatic approaches. Results: We developed a COBRA toolbox extension, deemed MetaboAnnotator, which facilitates the comprehensive annotation of metabolites with database independent and dependent identifiers, obtains molecular structure files, and calculates metabolite formula and charge at pH 7.2. The resulting metabolite annotations allow for subsequent cross-mapping between reconstructions and mapping of, e.g., metabolomic data. Availability and Implementation: MetaboAnnotator and tutorials are freely available at https://github.com/opencobra. Supplementary Information: Supplementary data are available at Bioinformatics online. (© The Author(s) 2022. Published by Oxford University Press.)
Databáze:	MEDLINE
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