Appropriate probe search method to specify groups in higher taxonomic ranks

A new method for procedures using a computer to find out useful candidates for probes discriminating a certain group in higher ranks of bacteria is presented. In order to make the search of the probes systematic, two indices are proposed, i.e., Coincidence Ratio Inside Group (CRIG) and Coincidence Number Outside Group (CNOG), which indicate the rate of matching of probes inside or outside group respectively. Using two indices, allowance grades indicating usefulness of arbitrary sequence as a probe are defined from 9 (5 in species) to 0. Its application to the 16S rRNA gene of 2206 bacterial species selected from the Ribosomal Database Project (RDP-II) (J.R. Cole et al., Nucleic Acids Res. 31: 442-443, 2003) is shown. Small nucleotide sequences of the length L (L = 15, 19, 23) were searched from about 550 bases. As a result of computer calculations, appropriate probes are found in all taxonomic ranks, in addition, it is found that 95% of genera can be identified uniquely. The method is useful for DNA chips or targeted PCR which can select a desirable bacteria set in any taxonomic rank. The method is in principle deterministic, and widely applied to any type of nucleotide sequences.