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

Bioinformatics, vol. 38, pp. 4831–4832

Abstract

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.

Authors 3

1. Ines Thiele corresponding

   Ollscoil na Gaillimhe – University of Galway · University College Cork · APC Microbiome Institute

   Affiliation as printed

   APC Microbiome Ireland, University College Cork , Cork T12K8AF, Ireland

   Division of Microbiology, University of Galway , Galway H91TK33, Ireland

   Ryan Institute, University of Galway , Galway H91TK33, Ireland

   School of Medicine, University of Galway , Galway H91TK33, Ireland

2. German Preciat Aachen Analytical BioSciences Division Leiden Academic Centre for Drug Research

   Leiden University

   Affiliation as printed

   Analytical BioSciences Division, Leiden Academic Centre for Drug Research, Leiden University , 2311 EZ, The Netherlands

3. Ronan M. T. Fleming Aachen Analytical BioSciences Division Leiden Academic Centre for Drug Research

   Leiden University · Ollscoil na Gaillimhe – University of Galway

   Affiliation as printed

   Analytical BioSciences Division, Leiden Academic Centre for Drug Research, Leiden University , 2311 EZ, The Netherlands

   School of Medicine, University of Galway , Galway H91TK33, Ireland