Details of assembly methods and in silico genotyping for *Salmonella* ===================================================================== * **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 | 3,002 Loci | 21,065 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 `Kidgell et al (2002) Infection, Genetics and Evolution. 2(1) 39-45`_. Genes included in 7 gene MLST (together with the length of sequence used for MLST taken from table 1 in the above cited paper): ==== =============== ====== Gene Name/ Locus Tag Length ==== =============== ====== thrA STY0002 501 purE STY0582 399 sucA STY0779 501 hisD STY2281 501 aroC STY2616 501 hemD STY3622 432 dnaN STY3941 501 ==== =============== ====== 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 .. _Kidgell et al (2002) Infection, Genetics and Evolution. 2(1) 39-45: http://mlst.warwick.ac.uk/mlst/mlst/mlst/dbs/Ecoli/AGroup/team/markPDF/5.pdf .. _`Achtman et al. (2012) PLoS Pathog 8(6): e1002776`: http://doi.org/10.1371/journal.ppat.1002776 .. _`Jolley et al. 2012 Microbiology 158:1005-15`: http://www.ncbi.nlm.nih.gov/pubmed/22282518