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Mycobacteria Genomics

This site uses two linked databases powered by the BIGSdb genomics platform. The sequence definition database contains allele sequence and MLST profile definitions whereas the isolate database contains provenance and epidemiological information. Further details about BIGSdb can be found in Jolley & Maiden 2010, BMC Bioinformatics 11:595.

This database contains genome sequence data assembled from public archives analysed by whole genome MLST (wgMLST).

The Mycobacteria MLST scheme has been developed by Granger Sutton and colleagues at the J. Craig Venter Institute, MD, USA, and has been funded in whole or part with federal funds from the National Institute of Allergy and Infectious Diseases, National Institutes of Health, Department of Health and Human Services under Award Number U19AI110819. The scheme has been designed for use with WGS data so no primer sequences are currently available.

Genome database curated by Sofia Hauck. The MLST scheme is curated by Lauren Brinkac

Citing the database

The preferred format for citing this website in publications is:

This publication made use of the PubMLST Mycobacteria genome database (https://pubmlst.org/ mycobacteria/) sited at the University of Oxford (Jolley et al. Wellcome Open Res 2018, 3:124 [version 1; referees: 2 approved]). The development of this site has been funded by the Wellcome Trust.

Status

Sequence database
Sequences: 292,234
Profiles:
Core genome (H37Rv ref vs 19 finished species): 5,626
MLST: 839

Isolate database
Isolates: 9,425
Last updated: 2017-08-29