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• W2891078715 startingPage "124" @default.
• W2891078715 abstract "The PubMLST.org website hosts a collection of open-access, curated databases that integrate population sequence data with provenance and phenotype information for over 100 different microbial species and genera. Although the PubMLST website was conceived as part of the development of the first multi-locus sequence typing (MLST) scheme in 1998 the software it uses, the Bacterial Isolate Genome Sequence database (BIGSdb, published in 2010), enables PubMLST to include all levels of sequence data, from single gene sequences up to and including complete, finished genomes. Here we describe developments in the BIGSdb software made from publication to June 2018 and show how the platform realises microbial population genomics for a wide range of applications. The system is based on the gene-by-gene analysis of microbial genomes, with each deposited sequence annotated and curated to identify the genes present and systematically catalogue their variation. Originally intended as a means of characterising isolates with typing schemes, the synthesis of sequences and records of genetic variation with provenance and phenotype data permits highly scalable (whole genome sequence data for tens of thousands of isolates) means of addressing a wide range of functional questions, including: the prediction of antimicrobial resistance; likely cross-reactivity with vaccine antigens; and the functional activities of different variants that lead to key phenotypes. There are no limitations to the number of sequences, genetic loci, allelic variants or schemes (combinations of loci) that can be included, enabling each database to represent an expanding catalogue of the genetic variation of the population in question. In addition to providing web-accessible analyses and links to third-party analysis and visualisation tools, the BIGSdb software includes a RESTful application programming interface (API) that enables access to all the underlying data for third-party applications and data analysis pipelines." @default.
• W2891078715 created "2018-09-27" @default.
• W2891078715 creator A5042779393 @default.
• W2891078715 creator A5043485383 @default.
• W2891078715 creator A5064855716 @default.
• W2891078715 date "2018-09-24" @default.
• W2891078715 modified "2023-10-09" @default.
• W2891078715 title "Open-access bacterial population genomics: BIGSdb software, the PubMLST.org website and their applications" @default.
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• W2891078715 doi "https://doi.org/10.12688/wellcomeopenres.14826.1" @default.
• W2891078715 hasPubMedCentralId "https://www.ncbi.nlm.nih.gov/pmc/articles/6192448" @default.

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