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08:03
Heuristic Mining of Hierarchical Genotypes and Accessory Genome Loci in Bacterial Populations
Published on: December 7, 2021
Rapid pair-wise synteny analysis of large bacterial genomes using web-based GeneOrder4.0
Padmanabhan Mahadevan1, Donald Seto
1Department of Bioinformatics and Computational Biology, 10900 University Blvd,, MSN 5B3, George Mason University, Manassas, VA 20110, USA. dseto@gmu.edu.
BMC Research Notes
|February 25, 2010
Summary
GeneOrder4.0 is a user-friendly, web-based tool for bacterial comparative genomics. It rapidly analyzes synteny and gene order, aiding researchers in mining large whole genome sequence databases.
Area of Science:
- Genomics
- Bioinformatics
Background:
- Increasing whole genome sequence data requires accessible analysis tools.
- Web-based tools offer platform independence for biologists without programming expertise.
Purpose of the Study:
- To present GeneOrder4.0, an updated web-based tool for bacterial comparative genomics.
- To facilitate user-friendly analysis of synteny and gene order.
Main Methods:
- Development of a web-based software application.
- Implementation of "on-the-fly" synteny analysis using protein similarity scores.
- Visualization of genomic data for comparative analysis.
Main Results:
- GeneOrder4.0 enables rapid "on-the-fly" synteny and gene order analysis for bacterial genomes (approx. 8 Mb).
- The tool visualizes synteny by plotting protein similarity scores between genomes.
- It provides visual annotation of hypothetical proteins using updated genomic data.
Conclusions:
- GeneOrder4.0 is a user-friendly web application for rapid analysis of bacterial genome synteny and gene order.
- The updated tool supports the analysis of large bacterial genomes, catering to wet-bench researchers.
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