ORMA: a tool for identification of species-specific variations in 16S rRNA gene and oligonucleotides design

Severgnini, Marco; Cremonesi, Paola; Consolandi, Clarissa; Caredda, Giada; De Bellis, Gianluca; Castiglioni, Bianca

In particular, 16S rRNA gene sequences have been used to resolve bacterial phylogeny and taxonomy issues in different contexts. The DNA sequence coding for the small ribosomal subunit has been by far the most common genetic marker employed by the scientific community, because of: (i) its presence in almost all bacteria, often existing as a multi-gene family, or operons; (ii) the function of the 16S rRNA gene has not changed over time, suggesting that random sequence changes are an accurate measure of time (evolution); and (iii) the 16S rRNA gene (more than 1500 bp) is large enough for informatics purposes (1) with large stretches of conserved regions and few different loci.