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

Overall structure. ORMA overall structure is tree-like, with a main function that, sequentially, recalls all the side scripts needed to perform each requested operation. The software also comprises a series of scripts for retrieving oligonucleotide sequences, quality-check them and design probes for different applications, such as Ligase Detection Reaction (LDR) or Minisequencing/Primer Extension probes. The overall procedure is accomplished in four main steps (Figure 1, Supplementary Figure 1 ): (i) sequence importing and processing; (ii) discriminating positions finding; (iii) designing of the candidate probes, starting from the positions found and (iv) ranking (i.e. assignment of a quality score to each) and exporting of the candidates (in tabular format).