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Phylogenomic clustering for selecting non-redundant genomes for comparative genomics
Gabriel Moreno-Hagelsieb1, Zilin Wang, Stephanie Walsh
1Department of Biology and Department of Mathematics, Wilfrid Laurier University, Waterloo, ON N2L 3C5, Canada. gmoreno@wlu.ca
Bioinformatics (Oxford, England)
|February 12, 2013
Summary
This study presents a new method and web server to cluster redundant genomes. This tool helps researchers create non-redundant genome datasets for comparative genomics analyses.
Area of Science:
- Genomics
- Bioinformatics
Background:
- Comparative genomics requires non-redundant genome datasets.
- Species-level redundancy is insufficient due to varying genomic similarity within and across species.
- Some genomes lack species identification, complicating dataset curation.
Purpose of the Study:
- To develop a method for clustering redundant genomes.
- To provide a web server for easy access to the redundancy clustering tool.
Main Methods:
- Implementation of a method for genome dataset clustering.
- Utilizing phylogenomic distance measures for similarity assessment.
- Development of a web server interface for the method.
Main Results:
- A functional method and web server for clustering redundant genomes have been implemented.
- The tool allows clustering at various thresholds based on phylogenomic distances.
Conclusions:
- The developed method and web server facilitate the creation of non-redundant genome datasets.
- This aids in more accurate comparative genomics analyses by addressing complex redundancy patterns.
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