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

ABSTRACT: 16S rRNA gene is one of the preferred targets for resolving species phylogenesis issues in microbiological-related contexts. However, the identification of single-nucleotide variations capable of distinguishing a sequence among a set of homologous ones can be problematic. Here we present ORMA (Oligonucleotide Retrieving for Molecular Applications), a set of scripts for discriminating positions search and for performing the selection of high-quality oligonucleotide probes to be used in molecular applications. Two assays based on Ligase Detection Reaction (LDR) are presented. First, a new set of probe pairs on cyanobacteria 16S rRNA sequences of 18 different species was compared to that of a previous study. Then, a set of LDR probe pairs for the discrimination of 13 pathogens contaminating b

SUBMITTER: Severgnini M 

PROVIDER: S-EPMC2760787 | biostudies-literature | 2009 Sep

REPOSITORIES: biostudies-literature