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A Web Tool for Generating High Quality Machine-readable Biological Pathways
Published on: February 8, 2017
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KIPEs3: Automatic annotation of biosynthesis pathways
Andreas Rempel1,2, Nancy Choudhary3, Boas Pucker3
1Genome Informatics, Faculty of Technology & Center for Biotechnology, Bielefeld University, Bielefeld, Germany.
Plos One
|November 16, 2023
Summary
KIPEs3 is an advanced tool for automatically annotating plant biosynthesis pathways, including flavonoids and carotenoids. It aids in identifying genes for pigment production, modification, and transport, supporting evolutionary and breeding research.
Area of Science:
- Plant biochemistry and molecular biology
- Bioinformatics and computational biology
Background:
- Flavonoids and carotenoids are crucial plant pigments involved in coloration and stress response.
- Their biosynthesis pathways are largely conserved but feature species-specific modifications.
Purpose of the Study:
- To introduce KIPEs3, an improved tool for automatic annotation of plant biosynthesis pathways.
- To expand KIPEs capabilities to include flavonoid and carotenoid biosynthesis, including decoration and transport genes.
- To facilitate analysis of large-scale genomic data for evolutionary and biotechnological insights.
Main Methods:
- Development and application of KIPEs3 for pathway annotation.
- Analysis of flavonoid biosynthesis in Arabidopsis thaliana, Capsella grandiflora, and Dioscorea dumetorum.
- Analysis of carotenoid biosynthesis in Arabidopsis thaliana, Capsella grandiflora, Dioscorea dumetorum, and Daucus carota.
Main Results:
- KIPEs3 successfully identified core biosynthesis players and candidates for flavonoid decoration and transport.
- Demonstrated the tool's applicability to both flavonoid and carotenoid pathways across multiple plant species.
- Validated KIPEs3's functionality and ease of use through case studies.
Conclusions:
- KIPEs3 is a robust and accessible online service for high-quality, large-scale plant biosynthesis pathway analysis.
- The tool supports the identification of candidate genes for evolutionary studies and breeding applications.
- KIPEs3 empowers researchers without extensive bioinformatics experience to analyze complex plant genomic data.
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