Details of assembly methods and in silico genotyping for Moraxella

  • 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)
8 Loci 53 Loci
Conserved Housekeeping genes Ribosomal proteins
Highly conserved; Low resolution Highly conserved; Medium resolution
Different scheme for each species/genus Single scheme across tree of life

Note that more schemes are currently implemented for Salmonella, Escherichia and Yersinia (and it may be worth reviewing the relevant pages in the documentation for a broader comparison of schemes).

8 Gene MLST

Classic MLST scheme is described in Wirth et al (2007) Genome Res. 17: 1647-1656.

Genes included in 8 gene MLST (together with the length of sequence used for MLST taken from table 1 in the above cited paper):

Gene Length
ppa 393
mutY 426
trpE 372
efp 414
fumC 465
glyBeta 537
adk 471
abcZ 429

Ribosomal MLST (rMLST)