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A Web Tool for Generating High Quality Machine-readable Biological Pathways
Published on: February 8, 2017
FMM: a web server for metabolic pathway reconstruction and comparative analysis
Chih-Hung Chou1, Wen-Chi Chang, Chih-Min Chiu
1Institute of Molecular Medicine and Bioengineering, National Chiao Tung University, Hsin-Chu 300, Taiwan, Republic of China.
Nucleic Acids Research
|April 30, 2009
Summary
The FMM web server reconstructs metabolic pathways between species using KEGG data. This tool aids synthetic biology in producing valuable compounds like drugs and biofuels.
Area of Science:
- Synthetic Biology
- Metabolic Engineering
- Bioinformatics
Background:
- Synthetic Biology aims to understand and engineer biological systems.
- Developing bio-orthogonal systems with novel functions is a key objective.
- Reconstructing metabolic pathways is crucial for engineering new cellular functions.
Purpose of the Study:
- To develop a web server, FMM (From Metabolite to Metabolite), for reconstructing metabolic pathways.
- To provide novel visualizations for connecting different KEGG maps.
- To facilitate applications in Synthetic Biology and Metabolic Engineering.
Main Methods:
- Utilized the Kyoto Encyclopedia of Genes and Genomes (KEGG) database.
- Integrated other relevant biological databases.
- Developed novel graphical representations for metabolic pathways (local and global views).
Main Results:
- Successfully developed the FMM web server for metabolic pathway reconstruction.
- Implemented novel methods for visualizing connections between KEGG maps.
- Enabled comparative pathway analysis for gene identification.
Conclusions:
- FMM is a valuable tool for Synthetic Biology and Metabolic Engineering.
- Facilitates the production of valuable metabolites, including drugs and biofuels.
- Supports the identification of genes for transfer between organisms to engineer new metabolic capabilities.
