4.7 Article

MPA_Pathway_Tool: User-Friendly, Automatic Assignment of Microbial Community Data on Metabolic Pathways

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出版社

MDPI
DOI: 10.3390/ijms222010992

关键词

omics; web application; pathway generation; pathway mapping; metaproteomics; bioinformatics

资金

  1. German Federal Ministry of Education and Research [031L0103]

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The taxonomic and functional characterization of microbial communities from diverse environments is increasingly important, with researchers using multi-omics methods to assign genes, transcripts, or proteins to biological pathways. The MPA_Pathway_Tool is a new web application that helps users create and map microbial community data onto specific pathways for better understanding of their functions.
Taxonomic and functional characterization of microbial communities from diverse environments such as the human gut or biogas plants by multi-omics methods plays an ever more important role. Researchers assign all identified genes, transcripts, or proteins to biological pathways to better understand the function of single species and microbial communities. However, due to the versality of microbial metabolism and a still-increasing number of newly biological pathways, linkage to standard pathway maps such as the KEGG central carbon metabolism is often problematic. We successfully implemented and validated a new user-friendly, stand-alone web application, the MPA_Pathway_Tool. It consists of two parts, called 'Pathway-Creator' and 'Pathway-Calculator'. The 'Pathway-Creator' enables an easy set-up of user-defined pathways with specific taxonomic constraints. The 'Pathway-Calculator' automatically maps microbial community data from multiple measurements on selected pathways and visualizes the results. The MPA_Pathway_Tool is implemented in Java and ReactJS.

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