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Here we describe the Not-N algorithm, which is designed to identify small sets of genetic markers diagnostic for user-specified subsets of known genetic variants. The algorithm does not treat the user-specified subset and the remaining genetic variants equally. Rather Not-N analysis is designed to underpin assays that provide 0% false negatives, which is very important for e.g. diagnostic procedures for clinically significant subgroups within microbial species.<\/jats:p><\/jats:sec><jats:sec><jats:title>Results<\/jats:title><jats:p>The Not-N algorithm has been incorporated into the \"Minimum SNPs\" computer program and used to derive genetic markers diagnostic for multilocus sequence typing-defined clonal complexes, hepatitis C virus (HCV) subtypes, and phylogenetic clades defined by comparative genome hybridization (CGH) data for<jats:italic>Campylobacter jejuni<\/jats:italic>,<jats:italic>Yersinia enterocolitica<\/jats:italic>and<jats:italic>Clostridium difficile<\/jats:italic>.<\/jats:p><\/jats:sec><jats:sec><jats:title>Conclusion<\/jats:title><jats:p>Not-N analysis is effective for identifying small sets of genetic markers diagnostic for microbial sub-groups. The best results to date have been obtained with CGH data from several bacterial species, and HCV sequence data.<\/jats:p><\/jats:sec>","DOI":"10.1186\/1471-2105-8-278","type":"journal-article","created":{"date-parts":[[2007,8,2]],"date-time":"2007-08-02T18:18:26Z","timestamp":1186078706000},"update-policy":"http:\/\/dx.doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":24,"title":["Computer-aided identification of polymorphism sets diagnostic for groups of bacterial and viral genetic variants"],"prefix":"10.1186","volume":"8","author":[{"given":"Erin P","family":"Price","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"John","family":"Inman-Bamber","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Venugopal","family":"Thiruvenkataswamy","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Flavia","family":"Huygens","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Philip M","family":"Giffard","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2007,8,1]]},"reference":[{"key":"1650_CR1","doi-asserted-by":"publisher","first-page":"382","DOI":"10.3201\/eid0703.017303","volume":"7","author":"B Swaminathan","year":"2001","unstructured":"Swaminathan B, Barrett TJ, Hunter SB, Tauxe RV, CDC PulseNet Task Force: PulseNet: the molecular subtyping network for foodborne bacterial disease surveillance, United States. 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