ORMA represents a good alternative solution to the troublesome problem of searching specific positions within a large set of homologous 16S rRNA sequences and provides tools for performing a series of probe-related operations, such as sequence retrieval, filtering and scoring, allowing the user to have a set of candidates on which the actual and definitive selection can be done. The calculation on intra-and inter-group scores allows the selection of highly specific probes for molecular applications, covering the highest number of species of the positive set and having the lowest interaction with the negative set.