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  Concepts and software for a rational design of polynucleotide probes

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

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Moraru, C.1, Author           
Moraru, G.1, Author           
Fuchs, B. M.1, Author           
Amann, R.1, Author           
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1Department of Molecular Ecology, Max Planck Institute for Marine Microbiology, Max Planck Society, ou_2481696              

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 Abstract: 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 GenBank Taxonomy Extractor (GTE), a Polynucleotide Probe Designer (PPD) and a Hybridization Parameters Calculator (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.

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Language(s): eng - English
 Dates: 2011-02
 Publication Status: Issued
 Pages: 10
 Publishing info: -
 Table of Contents: -
 Rev. Type: Peer
 Identifiers: eDoc: 574035
ISI: 000287144400022
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Title: Environmental Microbiology
  Other : Environmental Microbiology and Environmental Microbiology Reports
Source Genre: Journal
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Publ. Info: Oxford, England : Blackwell Science
Pages: - Volume / Issue: 3 (1) Sequence Number: - Start / End Page: 69 - 78 Identifier: ISSN: 1462-2912
CoNE: https://pure.mpg.de/cone/journals/resource/959328105031