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Updated: Jul 3, 2026

Development and Testing of Species-specific Quantitative PCR Assays for Environmental DNA Applications

Development and Testing of Species-specific Quantitative PCR Assays for Environmental DNA Applications

Published on: November 5, 2020

probeCheck--a central resource for evaluating oligonucleotide probe coverage and specificity.

Alexander Loy¹, Roland Arnold, Patrick Tischler

¹Department of Microbial Ecology, Universität Wien, Althanstrasse 14, A-1090 Wien, Austria.

Environmental Microbiology

|July 24, 2008

Summary

ProbeCheck is a web server for evaluating DNA probes and primers against microbial gene databases. It assesses specificity, coverage, and binding stability using integrated tools and multiple databases.

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Area of Science:

Microbial Ecology
Bioinformatics
Molecular Biology

Background:

Oligonucleotide probes and primers are essential tools in molecular biology for detecting and amplifying specific DNA sequences.
Accurate evaluation of probe and primer specificity and coverage is crucial for reliable experimental results.
Existing tools may lack comprehensive database integration or detailed binding stability analysis.

Purpose of the Study:

To introduce probeCheck, a web server for rapid and comprehensive evaluation of probes and primers.
To provide users with a flexible platform for assessing specificity, coverage, and binding stability against diverse databases.
To integrate multiple bioinformatics tools for a holistic analysis of oligonucleotide performance.

Main Methods:

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Last Updated: Jul 3, 2026

Development and Testing of Species-specific Quantitative PCR Assays for Environmental DNA Applications

Development and Testing of Species-specific Quantitative PCR Assays for Environmental DNA Applications

Published on: November 5, 2020

Kinetic Screening of Nuclease Activity using Nucleic Acid Probes

Kinetic Screening of Nuclease Activity using Nucleic Acid Probes

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Developed probeCheck web server integrating an online ARB probe match tool.

Incorporated free energy (DeltaG) calculations for assessing theoretical binding stabilities.

Enabled querying of 24 sequence collections, including RDP II, Greengenes, SILVA, and FGP/R.

Linked probeCheck with external tools like NCBI BLAST and probeBase for extended analysis.

Main Results:

ProbeCheck offers rapid specificity and coverage evaluations for probes and primers.
Calculates theoretical binding stabilities (DeltaG) for perfect and mismatched hybrids.
Provides detailed output including accession numbers, taxonomy, and database links.
Offers customizable filtering options for tailored results.

Conclusions:

ProbeCheck serves as a multifunctional platform for evaluating oligonucleotide probes and primers.
It enhances flexibility by allowing users to choose databases and analysis options.
The server facilitates the assessment of both published and newly designed probes and primers.