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 :doc:`here ` * **For a general description of the in silico typing method**, see :doc:`here ` +---------------------+--------------------+-------------------+-------+ | MLST – Classic | Ribosomal MLST | Core Genome MLST | Whole | | | (Jolley, 2012) | | Genom | | | | | e | | | | | MLST | +=====================+====================+===================+=======+ | 7 Loci | 51 Loci | 1,553 Loci | 19,53 | | | | | 1 | | | | | Loci | +---------------------+--------------------+-------------------+-------+ | Conserved | Ribosomal proteins | Core genes | Any | | Housekeeping genes | | | codin | | | | | g | | | | | seque | | | | | nce | +---------------------+--------------------+-------------------+-------+ | Highly conserved; | Highly conserved; | Variable; High | Highl | | Low resolution | Medium resolution | resolution | y | | | | | varia | | | | | ble; | | | | | Extre | | | | | me | | | | | resol | | | | | ution | +---------------------+--------------------+-------------------+-------+ | Different scheme | Single scheme | Different scheme | Diffe | | for each | across tree of | for each | rent | | species/genus | life | species/genus | 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): ==== ====== Gene Length ==== ====== adk 389 argA 361 aroA 357 glnA 338 thrA 342 tmk 375 trpE 465 ==== ====== 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): ==== ====== Gene Length ==== ====== aarF 500 dfp 455 galR 500 glnS 442 hemA 490 speA 452 rfaE 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 .. _Laukkanen-Ninios et al (2011) Environ. Microbiol. 13(12), 3114-3127: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3988354/ .. _Hall et al (2015) J. Clin. Microbiol. 53(1), 35-42: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4290955/ .. _`Jolley et al. 2012 Microbiology 158:1005-15`: http://www.ncbi.nlm.nih.gov/pubmed/22282518