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 :doc:`here ` * **For a general description of the in silico typing method**, see :doc:`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) ---------------------- - **rMLST** is Copyright © 2010-2016, University of Oxford. rMLST is described in `Jolley et al. 2012 Microbiology 158:1005-15`_. .. _please click here: EnteroBase%20Backend%20Pipeline%3A%20nomenclature .. _Salmonella: Salmonella%20Statistics .. _Escherichia: Escherichia%20Statistics .. _Yersinia: Yersinia%20Statistics .. _`Wirth et al (2007) Genome Res. 17: 1647-1656`: http://mlst.warwick.ac.uk/mlst/AGroup/team/markPDF/37.pdf .. _`Jolley et al. 2012 Microbiology 158:1005-15`: http://www.ncbi.nlm.nih.gov/pubmed/22282518