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Updated: Feb 3, 2026
08:03
Heuristic Mining of Hierarchical Genotypes and Accessory Genome Loci in Bacterial Populations
Published on: December 7, 2021
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Open-access bacterial population genomics: BIGSdb software, the PubMLST.org website and their applications
Keith A Jolley1, James E Bray1, Martin C J Maiden1
1Department of Zoology, University of Oxford, Oxford, OX1 3PS, UK.
Wellcome Open Research
|October 23, 2018
Summary
PubMLST.org provides open-access microbial population genomics data using BIGSdb software. This platform integrates sequence data with phenotypes for diverse applications, including antimicrobial resistance prediction.
Area of Science:
- Microbial genomics
- Bioinformatics
- Population genetics
Background:
- PubMLST.org hosts curated databases for over 100 microbial species.
- The Bacterial Isolate Genome Sequence database (BIGSdb) software underpins PubMLST, supporting various sequence data levels.
Purpose of the Study:
- To describe developments in BIGSdb software from its publication to June 2018.
- To demonstrate the platform's utility for microbial population genomics applications.
Main Methods:
- Gene-by-gene analysis of microbial genomes.
- Sequence annotation and curation to identify genes and catalogue variations.
- Integration of sequence data with provenance and phenotype information.
Main Results:
- BIGSdb enables scalable analysis of tens of thousands of isolates.
- The platform facilitates prediction of antimicrobial resistance and vaccine cross-reactivity.
- It supports functional analysis of genetic variants linked to phenotypes.
Conclusions:
- BIGSdb offers a flexible platform for microbial population genomics with no limitations on data inclusion.
- The software provides web-accessible analyses and a RESTful API for data access.
- PubMLST.org serves as a valuable resource for addressing functional questions in microbial genomics.
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