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Concepts and software for a rational design of polynucleotide probes
Author(s) -
Moraru Cristina,
Moraru Gabriel,
Fuchs Bernhard M.,
Amann Rudolf
Publication year - 2011
Publication title -
environmental microbiology reports
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.229
H-Index - 69
ISSN - 1758-2229
DOI - 10.1111/j.1758-2229.2010.00189.x
Subject(s) - polynucleotide , rational design , gene , oligonucleotide , biology , computational biology , genetics , fish <actinopterygii> , microbiology and biotechnology , fishery
Summary Fluorescence in situ hybridization (FISH) of genes and mRNA is most often based on polynucleotide probes. However, so far there was no published framework for the rational design of polynucleotide probes. The well‐established concepts for oligonucleotide probe design cannot be transferred to polynucleotides. Due to the high allele diversity of genes, a single probe is not sufficient to detect all alleles of a gene. Therefore, the main objective of this study was to develop a concept and software (PolyPro) for rational design of polynucleotide probe mixes to target particular genes. PolyPro consists of three modules: a G enBank T axonomy E xtractor (GTE), a P olynucleotide P robe D esigner (PPD) and a H ybridization P arameters C alculator (HPC). The new 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.