Details of assembly methods and in silico genotyping for *Escherichia* ====================================================================== * **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 | Core Genome | Whole Genome | | | (Jolley, 2012) | MLST | MLST | +=================+================+===============+=================+ | 7 Loci | 51 Loci | 2,513 Loci | 25,002 Loci | +-----------------+----------------+---------------+-----------------+ | Conserved | Ribosomal | Core genes | Any coding | | Housekeeping | proteins | | sequence | | genes | | | | +-----------------+----------------+---------------+-----------------+ | Highly | Highly | Variable; | Highly | | conserved; Low | conserved; | High | variable; | | resolution | Medium | resolution | Extreme | | | resolution | | resolution | +-----------------+----------------+---------------+-----------------+ | Different | Single scheme | Different | Different | | scheme for each | across tree of | scheme for | scheme for each | | species/genus | life | each | species/genus | | | | species/genus | | +-----------------+----------------+---------------+-----------------+ 7 Gene MLST ----------- Classic MLST scheme is described in `Wirth et al (2006) Mol. Microbiol. 60(5), 1136-1151`_. Genes included in 7 gene MLST (together with the length of sequence used for MLST taken from figure 1 in the above cited paper): ==== ====== Gene Length ==== ====== adk 536 fumC 469 gyrB 460 icd 518 mdh 452 recA 510 purA 478 ==== ====== 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 .. _Wirth et al (2006) Mol. Microbiol. 60(5), 1136-1151: http://onlinelibrary.wiley.com/doi/10.1111/j.1365-2958.2006.05172.x/full .. _`Jolley et al. 2012 Microbiology 158:1005-15`: http://www.ncbi.nlm.nih.gov/pubmed/22282518