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Yersinia pestis

The Yersinia pestis database is based upon the data published by Pourcel et al., BMC microbiology 2004, with minor modifications as described on this site.

data source and modifications

The data presented here is as can be downloaded from Pourcel et al., BMC microbiology 2004 with the following minor modifications : 1-ms46 was incorrectly considered as an 17 bp repeat unit whereas it varies as a 7 bp repeat unit. The data has been recoded accordingly (see Li et al., PlosOne 2009 for more details). Consequently, the allele calling code is now ms46_7bp_252bp_5U (which means, the locus is considered as a 7 bp repeat unit locus, and a 252 bp PCR product for this locus in (...)

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Tips for genotyping

Polymorphic Tandem repeat loci for Yersinia pestis typing Three groups have evaluated tandem repeat loci for typing Y. pestis. These studies were reported in Le Flèche et al. 2001, Klevytska et al., 2001, Li et al., 2013 and evaluated in a number of publications in the past few years. The first report and subsequent work described 25 loci. The second report and associated work corresponds to 43 loci. Six loci are shared in these two sets (as shown in Pourcel et al., 2004), markers (...)

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