MPA_Pathway_Tool: User-Friendly, Automatic Assignment of Microbial Community Data on Metabolic Pathways
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...
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| Format: | Article |
| Language: | English |
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MDPI AG
2021-10-01
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| Series: | International Journal of Molecular Sciences |
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| Online Access: | https://www.mdpi.com/1422-0067/22/20/10992 |
| _version_ | 1797514419286048768 |
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| author | Daniel Walke Kay Schallert Prasanna Ramesh Dirk Benndorf Emanuel Lange Udo Reichl Robert Heyer |
| author_facet | Daniel Walke Kay Schallert Prasanna Ramesh Dirk Benndorf Emanuel Lange Udo Reichl Robert Heyer |
| author_sort | Daniel Walke |
| collection | DOAJ |
| description | 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. |
| first_indexed | 2024-03-10T06:31:21Z |
| format | Article |
| id | doaj.art-fece8935db47498893712acdd06438ba |
| institution | Directory Open Access Journal |
| issn | 1661-6596 1422-0067 |
| language | English |
| last_indexed | 2024-03-10T06:31:21Z |
| publishDate | 2021-10-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | International Journal of Molecular Sciences |
| spelling | doaj.art-fece8935db47498893712acdd06438ba2023-11-22T18:31:57ZengMDPI AGInternational Journal of Molecular Sciences1661-65961422-00672021-10-0122201099210.3390/ijms222010992MPA_Pathway_Tool: User-Friendly, Automatic Assignment of Microbial Community Data on Metabolic PathwaysDaniel Walke0Kay Schallert1Prasanna Ramesh2Dirk Benndorf3Emanuel Lange4Udo Reichl5Robert Heyer6Bioprocess Engineering, Otto von Guericke University, Universitätsplatz 2, 39106 Magdeburg, GermanyBioprocess Engineering, Otto von Guericke University, Universitätsplatz 2, 39106 Magdeburg, GermanyDatabase and Software Engineering Group, Otto von Guericke University, Universitätsplatz 2, 39106 Magdeburg, GermanyBioprocess Engineering, Otto von Guericke University, Universitätsplatz 2, 39106 Magdeburg, GermanyBioprocess Engineering, Otto von Guericke University, Universitätsplatz 2, 39106 Magdeburg, GermanyBioprocess Engineering, Otto von Guericke University, Universitätsplatz 2, 39106 Magdeburg, GermanyBioprocess Engineering, Otto von Guericke University, Universitätsplatz 2, 39106 Magdeburg, GermanyTaxonomic 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.https://www.mdpi.com/1422-0067/22/20/10992omicsweb applicationpathway generationpathway mappingmetaproteomicsbioinformatics |
| spellingShingle | Daniel Walke Kay Schallert Prasanna Ramesh Dirk Benndorf Emanuel Lange Udo Reichl Robert Heyer MPA_Pathway_Tool: User-Friendly, Automatic Assignment of Microbial Community Data on Metabolic Pathways International Journal of Molecular Sciences omics web application pathway generation pathway mapping metaproteomics bioinformatics |
| title | MPA_Pathway_Tool: User-Friendly, Automatic Assignment of Microbial Community Data on Metabolic Pathways |
| title_full | MPA_Pathway_Tool: User-Friendly, Automatic Assignment of Microbial Community Data on Metabolic Pathways |
| title_fullStr | MPA_Pathway_Tool: User-Friendly, Automatic Assignment of Microbial Community Data on Metabolic Pathways |
| title_full_unstemmed | MPA_Pathway_Tool: User-Friendly, Automatic Assignment of Microbial Community Data on Metabolic Pathways |
| title_short | MPA_Pathway_Tool: User-Friendly, Automatic Assignment of Microbial Community Data on Metabolic Pathways |
| title_sort | mpa pathway tool user friendly automatic assignment of microbial community data on metabolic pathways |
| topic | omics web application pathway generation pathway mapping metaproteomics bioinformatics |
| url | https://www.mdpi.com/1422-0067/22/20/10992 |
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