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Article

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

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Bioprocess Engineering, Otto von Guericke University, Universitätsplatz 2, 39106 Magdeburg, Germany
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Database and Software Engineering Group, Otto von Guericke University, Universitätsplatz 2, 39106 Magdeburg, Germany
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Applied Biosciences and Process Engineering, Anhalt University of Applied Sciences, Microbiology, Bernburger Straße 55, 06354 Köthen, Germany
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Bioprocess Engineering, Max Planck Institute for Dynamics of Complex Technical Systems, Sandtorstraße 1, 39106 Magdeburg, Germany
*
Authors to whom correspondence should be addressed.
Academic Editor: Antonio Federico
Int. J. Mol. Sci. 2021, 22(20), 10992; https://doi.org/10.3390/ijms222010992
Received: 9 July 2021 / Revised: 2 October 2021 / Accepted: 6 October 2021 / Published: 12 October 2021
(This article belongs to the Section Molecular Informatics)
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. View Full-Text
Keywords: omics; web application; pathway generation; pathway mapping; metaproteomics; bioinformatics omics; web application; pathway generation; pathway mapping; metaproteomics; bioinformatics
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MDPI and ACS Style

Walke, D.; Schallert, K.; Ramesh, P.; Benndorf, D.; Lange, E.; Reichl, U.; Heyer, R. MPA_Pathway_Tool: User-Friendly, Automatic Assignment of Microbial Community Data on Metabolic Pathways. Int. J. Mol. Sci. 2021, 22, 10992. https://doi.org/10.3390/ijms222010992

AMA Style

Walke D, Schallert K, Ramesh P, Benndorf D, Lange E, Reichl U, Heyer R. MPA_Pathway_Tool: User-Friendly, Automatic Assignment of Microbial Community Data on Metabolic Pathways. International Journal of Molecular Sciences. 2021; 22(20):10992. https://doi.org/10.3390/ijms222010992

Chicago/Turabian Style

Walke, Daniel, Kay Schallert, Prasanna Ramesh, Dirk Benndorf, Emanuel Lange, Udo Reichl, and Robert Heyer. 2021. "MPA_Pathway_Tool: User-Friendly, Automatic Assignment of Microbial Community Data on Metabolic Pathways" International Journal of Molecular Sciences 22, no. 20: 10992. https://doi.org/10.3390/ijms222010992

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