Abstract: The present invention relates to methods for the design and/or production of a probe or primer that is capable of hybridizing to a plurality of sites in a sample comprising nucleic acid. Furthermore, the present invention provides methods for detecting and amplifying nucleic acid using such a probe or primer, for example, for identification of a strain, species or genera. Probe or primer sequences are determined by reference to codon usage bias of a target nucleic acid. In addition, the present invention provides methods for determining codon distribution and/or base pair distance between codons in a nucleic acid.

Abstract: The present invention relates to methods for the design and/or production of a probe or primer that is capable of hybridizing to a plurality of sites in a sample comprising nucleic acid. Furthermore, the present invention provides methods for detecting and amplifying nucleic acid using such a probe or primer, for example, for identification of a strain, species or genera. Probe or primer sequences are determined by reference to codon usage bias of a target nucleic acid. In addition, the present invention provides methods for determining codon distribution and/or base pair distance between codons in a nucleic acid.

Abstract: A set of oligonucleotide probes and method are disclosed for detecting a plurality of different target polynucleotides. The set includes a collection of different promiscuous probes each of which is capable of hybridizing to a target sequence shared between at least two of the target polynucleotides. At least one target polynucleotide comprises at least one target sequence that is shared with one or more other target polynucleotides. A predefined combination of promiscuous probes is capable of hybridizing to target sequences of said at least one target polynucleotide, wherein said predefined combination of probes provides specificity of detection of that target polynucleotide. Also disclosed are processes of identifying a set of target sequences for designing the set of oligonucleotide probes of the invention.