title: Strain/species-specific probe design for microbial identification microarrays.
abstract: Specific identification of microorganisms in the environment is important but challenging, especially at the species/strain level. Here, we have developed a novel k-mer-based approach to select strain/species-specific probes for microbial identification with diagnostic microarrays. Application of this approach to human microbiome genomes showed that multiple (≥10 probes per strain) strain-specific 50-mer oligonucleotide probes could be designed for 2,012 of 3,421 bacterial strains of the human microbiome, and species-specific probes could be designed for most of the other strains. The method can also be used to select strain/species-specific probes for sequenced genomes in any environments, such as soil and water.
authors.affiliation: Institute for Environmental Genomics, University of Oklahoma, Norman, Oklahoma, USA.
authors.forename: Qichao
authors.initials: Q
authors.lastname: Tu
authors.forename: Zhili
authors.initials: Z
authors.lastname: He
authors.forename: Ye
authors.initials: Y
authors.lastname: Deng
authors.forename: Jizhong
authors.initials: J
authors.lastname: Zhou
mesh_terms: D001419:Bacteria / Q000145:classification* / Q000235:genetics*; D005798:Genes, Bacterial; D006801:Humans; D054892:Metagenome; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D015345:Oligonucleotide Probes / Q000235:genetics*; D013045:Species Specificity
chemical_list: D015345:Oligonucleotide Probes