ArticleBMC bioinformatics2007
Computer-aided identification of polymorphism sets diagnostic for groups of bacterial and viral genetic variants.
Article in BMC bioinformatics, 2007. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.
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Who cites it
11 citing papers in PubMed.
- minSNPs: an R package for the derivation of resolution-optimised SNP sets from microbial genomic data.PeerJ · 2023Article
- Rapid high-resolution melting genotyping scheme for Escherichia coli based on MLST derived single nucleotide polymorphisms.Scientific reports · 2021Article
- EasyPrimer: user-friendly tool for pan-PCR/HRM primers design. Development of an HRM protocol on wzi gene for fast Klebsiella pneumoniae typing.Scientific reports · 2020Article
- Article
- Multicolor Melting Curve Analysis-Based Multilocus Melt Typing of Vibrio parahaemolyticus.PloS one · 2015Article
- A comparison of two informative SNP-based strategies for typing Pseudomonas aeruginosa isolates from patients with cystic fibrosis.BMC infectious diseases · 2014Article
- Developing diagnostic SNP panels for the identification of true fruit flies (Diptera: Tephritidae) within the limits of COI-based species delimitation.BMC evolutionary biology · 2013Article
- Software for selecting the most informative sets of genomic loci for multi-target microbial typing.BMC bioinformatics · 2013Article
- Epidemiological tracking and population assignment of the non-clonal bacterium, Burkholderia pseudomallei.PLoS neglected tropical diseases · 2011Article
- The utility of high-resolution melting analysis of SNP nucleated PCR amplicons--an MLST based Staphylococcus aureus typing scheme.PloS one · 2011Article
- Assignment of Streptococcus agalactiae isolates to clonal complexes using a small set of single nucleotide polymorphisms.BMC microbiology · 2008Article
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5 authors.
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Abstract
backgroundSingle 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.
resultsThe 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 Campylobacter jejuni, Yersinia enterocolitica and Clostridium difficile.
conclusionNot-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.
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