Computer-aided identification of polymorphism sets diagnostic for groups of bacterial and viral genetic variants

Background: Single nucleotide polymorphisms (SNPs) and genes that exhibit presence/absence variation have provided informative marker sets for bacterial and viral genotyping. Identification of marker sets optimised for these purposes has been based on maximal generalized discriminatory power as measured by Simpson's Index of Diversity, or on the ability to identify specific variants. 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. Results: The Not-N algorithm has been incorporated into the "Minimum SNPs" computer program and used to derive genetic markers diag...

• Type: Journal
• Year: 2007
• Where: BMCBI
• Authors: Erin P. Price, John Inman-Bamber, Venugopal Thiruvenkataswamy, Flavia Huygens, Philip M. Giffard
• Keywords: BMCBI 2007, Genetic Markers, Genetic Variants, Marker Sets