School of Medicine, University of Galway, Galway H91TK33, Ireland.
Ryan Institute, University of Galway, Galway H91TK33, Ireland.
Bioinformatics. 2022 Oct 14;38(20):4831-4832. doi: 10.1093/bioinformatics/btac596.
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.
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.
MetaboAnnotator and tutorials are freely available at https://github.com/opencobra.
Supplementary data are available at Bioinformatics online.
使用各种工具，已经为数千种生物体组装了基因组规模的代谢重建。然而，要比较和链接重建之间的代谢物，所需的代谢物注释仍然不完整。在这里，我们旨在使用各种数据库和化学生物信息学方法进一步扩展代谢物注释的覆盖范围。
我们开发了一个 COBRA 工具包扩展，称为 MetaboAnnotator，它可以方便地使用数据库独立和依赖标识符对代谢物进行全面注释，获取分子结构文件，并计算 pH 值为 7.2 时的代谢物公式和电荷。生成的代谢物注释允许在重建之间进行后续的交叉映射，例如代谢组学数据的映射。
MetaboAnnotator 和教程可在 https://github.com/opencobra 上免费获得。
补充数据可在 Bioinformatics 在线获得。
