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qPrimerDB: a thermodynamics-based gene-specific qPCR primer database for 147 organisms
Kun Lu1,2, Tian Li3, Jian He4,5
1College of Agronomy and Biotechnology, Southwest University, Beibei, Chongqing 400715, China.
Nucleic Acids Research
|October 5, 2017
Summary
qPrimerDB is a comprehensive database for designing and validating gene-specific primers for quantitative polymerase chain reaction (qPCR). It offers millions of primer pairs across 147 organisms, improving gene expression analysis accuracy and efficiency.
Area of Science:
- Molecular Biology
- Bioinformatics
- Genomics
Background:
- Quantitative polymerase chain reaction (qPCR) is crucial for gene expression analysis.
- High-quality primers are essential for successful qPCR experiments.
- Existing qPCR primer databases lack comprehensive coverage across diverse organisms.
Purpose of the Study:
- To develop qPrimerDB, a comprehensive database for gene-specific qPCR primer design and validation.
- To provide a user-friendly web interface for accessing pre-computed primer pairs.
- To support gene expression analysis across a wide range of organisms.
Main Methods:
- An automated workflow for gene-specific qPCR primer design.
- Thermodynamics-based validation of primer pair quality.
- Inclusion of 147 organisms, with millions of primer pairs available.
- Experimental validation of primer specificity and efficiency using qPCR assays and gel electrophoresis.
Main Results:
- qPrimerDB contains over 3.3 million optimal primer pairs and 47.7 million alternative primer pairs.
- The database covers 147 organisms, including human, mouse, zebrafish, yeast, and plants.
- Experimental validation confirmed the specificity and efficiency of selected primers.
- A web front-end facilitates easy access and batch downloading of primer data.
Conclusions:
- qPrimerDB is a valuable, time-saving resource for researchers conducting gene expression analysis.
- The database significantly expands the availability of high-quality qPCR primers.
- It is a routinely updated, publicly accessible resource for the scientific community.
