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GETPrime 2.0: gene- and transcript-specific qPCR primers for 13 species including polymorphisms
Fabrice P A David1,2, Jacques Rougemont3,2, Bart Deplancke4,5
1Bioinformatics and Biostatistics Core Facility, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland.
Nucleic Acids Research
|January 6, 2017
Summary
The GETPrime database now offers pre-computed qPCR primer pairs for 13 species, including 8 new ones, with enhanced specificity and polymorphism mapping for improved experimental accuracy.
Area of Science:
- Genomics
- Bioinformatics
- Molecular Biology
Background:
- Quantitative Polymerase Chain Reaction (qPCR) is a vital technique for gene expression analysis.
- Designing specific and efficient primers is crucial for accurate qPCR results.
- Existing primer databases may lack comprehensive species coverage or detailed variant information.
Purpose of the Study:
- To report a major upgrade (version 2.0) of the GETPrime database.
- To expand the database's utility by including more species and enhancing primer information.
- To improve the accuracy and reduce experimental error in qPCR studies.
Main Methods:
- Expanded the GETPrime database to include eight new species: yeast, chicken, macaque, chimpanzee, rat, platypus, pufferfish, and Anolis carolinensis.
- Updated the genomic reference to Ensembl v81 and redesigned the back-end database for automated species-independent data import.
- Implemented mapping of known polymorphisms to primers to aid in strain- or individual-specific targeting.
Main Results:
- GETPrime 2.0 now supports 13 species, significantly increasing its applicability.
- Primers are optimized for genome-wide specificity and selective amplification of splice variants.
- Polymorphism mapping (average of three per human primer) is now available, aiding in experimental error reduction.
Conclusions:
- The upgraded GETPrime database provides a more comprehensive and accurate resource for qPCR primer design across a wider range of species.
- Automated data import and polymorphism mapping streamline primer selection and enhance experimental reliability.
- The database architecture facilitates the straightforward inclusion of future genomic releases and species.
