Dec 15, 2010

BIGSdb: Scalable analysis of bacterial genome variation at the population level

BMC Bioinformatics
Keith A Jolley, Martin C J Maiden

Abstract

The opportunities for bacterial population genomics that are being realised by the application of parallel nucleotide sequencing require novel bioinformatics platforms. These must be capable of the storage, retrieval, and analysis of linked phenotypic and genotypic information in an accessible, scalable and computationally efficient manner. The Bacterial Isolate Genome Sequence Database (BIGSDB) is a scalable, open source, web-accessible database system that meets these needs, enabling phenotype and sequence data, which can range from a single sequence read to whole genome data, to be efficiently linked for a limitless number of bacterial specimens. The system builds on the widely used mlstdbNet software, developed for the storage and distribution of multilocus sequence typing (MLST) data, and incorporates the capacity to define and identify any number of loci and genetic variants at those loci within the stored nucleotide sequences. These loci can be further organised into 'schemes' for isolate characterisation or for evolutionary or functional analyses. Isolates and loci can be indexed by multiple names and any number of alternative schemes can be accommodated, enabling cross-referencing of different studies and approaches. L...Continue Reading

  • References56
  • Citations661

References

  • References56
  • Citations661

Citations

Mentioned in this Paper

Variable Number of Tandem Repeats
Neisseria meningitidis
Methicillin resistant Staphylococcus aureus (organism)
Genome
Vaccines
Spirodinium equi
Mrsa - Methicillin Resistant Staphylococcus Aureus Infection
Streptococcus
Bio-Informatics
Minisatellite Repeats

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