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Updated: Aug 14, 2026
08:03
Heuristic Mining of Hierarchical Genotypes and Accessory Genome Loci in Bacterial Populations
Published on: December 7, 2021
xBASE, a collection of online databases for bacterial comparative genomics
Roy R Chaudhuri1, Mark J Pallen
1Division of Immunity and Infection, University of Birmingham, Birmingham, UK.
Nucleic Acids Research
|December 31, 2005
Summary
The xBASE system extends the coliBASE schema to create new bacterial genome databases for various taxa. These databases offer user-friendly genome comparison and analysis tools for research.
Area of Science:
- Microbiology
- Bioinformatics
- Genomics
Background:
- The Escherichia coli database, coliBASE, provided a foundation for bacterial genomic information.
- A need existed for comprehensive genomic resources for diverse bacterial taxa beyond E. coli.
Purpose of the Study:
- To adapt the coliBASE schema for a broader range of bacterial species.
- To develop a unified system (xBASE) for accessing and comparing bacterial genomes.
- To introduce enhanced analytical features for genomic research.
Main Methods:
- Application of the coliBASE schema to create new databases for specific bacterial groups.
- Development of a web-based graphical interface for user-friendly access.
- Implementation of features such as whole genome displays, gene painting, pattern search, and batch BLAST.
Main Results:
- Creation of multiple specialized databases: CampyDB, PseudoDB, ClostriDB, RhizoDB, and MycoDB.
- Provision of tools for genome annotation and comparison.
- Introduction of novel features for motif identification and protein analysis.
Conclusions:
- The xBASE system successfully extends bacterial genomic data accessibility and analysis capabilities.
- These databases facilitate hypothesis generation for laboratory investigations.
- xBASE serves as a valuable resource for the microbiology and bioinformatics communities.
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