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CoMetGeNe: mining conserved neighborhood patterns in metabolic and genomic contexts
Alexandra Zaharia1, Bernard Labedan1, Christine Froidevaux1
1Laboratoire de Recherche en Informatique (LRI), CNRS, Université Paris-Sud, Université Paris-Saclay, Orsay, 91405, France.
BMC Bioinformatics
|January 12, 2019
Summary
CoMetGeNe identifies conserved metabolic and genomic neighborhood patterns by analyzing reaction chains catalyzed by neighboring genes. This tool aids in understanding gene conservation and discovering novel metabolic pathways across species.
Area of Science:
- Systems Biology
- Bioinformatics
- Genomics
Background:
- Systems biology requires integrative network mining to analyze large genomic datasets.
- Analyzing metabolic pathways alongside genomic context reveals patterns of reaction chains catalyzed by neighboring gene products.
- Identifying conserved patterns across species provides insights into evolutionary relationships.
Purpose of the Study:
- To introduce CoMetGeNe (COnserved METabolic and GEnomic NEighborhoods), a novel method for identifying conserved metabolic and genomic patterns.
- To utilize these patterns for assessing conservation across multiple prokaryotic species.
- To enhance genome annotation and discover alternative metabolic routes.
Main Methods:
- CoMetGeNe identifies maximal trails of reactions catalyzed by products of neighboring genes.
- Identified patterns are used to evaluate conservation across diverse prokaryotic species.
- The method facilitates interspecies comparisons for biological discovery.
Main Results:
- CoMetGeNe successfully identifies conserved metabolic and genomic neighborhood patterns.
- Interspecies comparisons improve genome annotation accuracy.
- The analysis reveals potential alternative metabolic pathways and novel gene orderings.
Conclusions:
- CoMetGeNe serves as an exploratory tool for genomic and metabolic analysis.
- It offers insights into the conservation of functionally related gene clusters.
- The open-source CoMetGeNe pipeline is publicly available for research use.
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