Details of assembly methods and in silico genotyping for Yersinia¶
- All MLST-like typing methods in EnteroBase are derived from a genome assembly of sequenced reads. For an explanation of this method, see here
- For a general description of the in silico typing method, see here
|MLST – Classic||Ribosomal MLST (Jolley, 2012)||Core Genome MLST||Whole Genom e MLST|
|7 Loci||53 Loci||1,553 Loci||19,53 1 Loci|
|Conserved Housekeeping genes||Ribosomal proteins||Core genes||Any codin g seque nce|
|Highly conserved; Low resolution||Highly conserved; Medium resolution||Variable; High resolution||Highl y varia ble; Extre me resol ution|
|Different scheme for each species/genus||Single scheme across tree of life||Different scheme for each species/genus||Diffe rent schem e for each speci es/ge nus|
7 Gene MLST¶
Achtman 7 gene MLST scheme¶
The Achtman 7 gene MLST scheme is described in Laukkanen-Ninios et al (2011) Environ. Microbiol. 13(12), 3114-3127.
Genes included in Achtman 7 gene MLST (together with the length of sequence used for MLST taken from table 3 in the above cited paper):
McNally 7 gene MLST scheme¶
The McNally 7 gene MLST scheme is described in Hall et al (2015) J. Clin. Microbiol. 53(1), 35-42.
Genes included in McNally 7 gene MLST (together with the length of sequence used for MLST taken from table 2 in the above cited paper):