Author: Severgnini, Marco; Cremonesi, Paola; Consolandi, Clarissa; Caredda, Giada; De Bellis, Gianluca; Castiglioni, Bianca
Title: ORMA: a tool for identification of species-specific variations in 16S rRNA gene and oligonucleotides design Document date: 2009_6_16
ID: vrd89yk0_41
Snippet: In silico checks versus public databases (e.g. RDP or BLAST) are necessary only in case of lack of a reference among the sequences imported in ORMA or when the species eventually present in the biological context under study are too many for being comprised into a reasonably small negative set (e.g. all the microorganisms potentially present in bovine milk). Appropriate experimental designs, comprising context-specific PCRs for reducing the molec.....
Document: In silico checks versus public databases (e.g. RDP or BLAST) are necessary only in case of lack of a reference among the sequences imported in ORMA or when the species eventually present in the biological context under study are too many for being comprised into a reasonably small negative set (e.g. all the microorganisms potentially present in bovine milk). Appropriate experimental designs, comprising context-specific PCRs for reducing the molecular complexity of the target can also be helpful. A complete set of major thermodynamic parameters are reported in the output, helping the researcher to carefully select the best probes. Our data assessed and demonstrated the performances of ORMA in designing probes for molecular applications on 16S rRNA gene and their feasibility for experimental use, with improved specificity and sensitivity.
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