PolyPro

Polynucleotide Probe Design software

When you are using this software, please cite:

Moraru, C., Moraru, G., Fuchs, B.M., and Amann, R. (2011) Concepts and software for a rational design of polynucleotide probes. Environ. Microbiol. Reports, 3: 69-78.

   In situ hybridization of genes and mRNA is most often based on polynucleotide probes. However, the specificity of polynucleotide probes has not been thoroughly investigated and a rational probe design concept was still missing, because the well established concept for oligonucleotide probe design cannot be transferred to polynucleotides.
   We recently developed a concept and software (PolyPro) for rational design of polynucleotide probe mixes to identify particular genes in defined taxa. PolyPro consists of three modules: a GenBank Taxonomy Extractor (GTE), a Polynucleotide Probe Designer (PPD) and a Hybridization Parameters Calculator (HPC).

   The new probe design concept proposes the construction of defined polynucleotide mixes to target the habitat specific sequence diversity of a particular gene. The concept and the software are intended as a first step towards a more frequent application of polynucleotides for in situ identification of mRNA and genes in environmental microbiology.

   The PolyPro is a freeware program which runs on Windows platforms. It can be downloaded from here.

Additional information about the probe design concept and the PolyPro software can be found in the following publications:

1. Moraru, C., Moraru, G., Fuchs, B.M., and Amann, R. (2011) Concepts and software for a rational design of polynucleotide probes. Environ. Microbiol. Reports, 3: 69-78.

This paper describes in detail each of the three modules of the PolyPro software and the algorithms within.

2. Moraru, C., Lam, P., Fuchs, B.M., Kuypers, M.M.M. and Amann, R. (2010) GeneFISH – an in situ technique for linking gene presence and cell identity in environmental microorganisms. Environ. Microbiol. 12: 3057-3073.

In the Supporting Information of this paper, an example of the step by step design of polynucleotide probes for the amoA gene can be found.