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ExonSurfer

A web-tool for exon-specific primer design

About ExonSurfer

ExonSurfer is a web-tool for designing high-specificity exon junction binding transcript primers for qPCR, using the Ensembl database and the blastn algorithm. It combines all the steps of transcript-specific primer design, such as target selection to exclude other transcripts of the same gene, avoiding common polymorphic regions, and enables specificity and self-complementarity verification.

ExonSurfer simplifies the primer design process, while providing the user with a variety of options to customize the design to best suit their needs. In conclusion, this tool ensures high specificity and low non-specific binding of the primers, making ExonSurfer an essential tool for transcript-specific detection.

Design Primers

Create primers for your favorite species and gene using ExonSurfer's user-friendly interface and customizable parameters.


Upload Custom Transcript Files

ExonSurfer supports custom transcript information. Upload your own FASTA or GenBank file if your gene or transcript isn't available in the Ensembl database.

ExonSurfer: Code Availability and Usage

ExonSurfer is not only a versatile web-tool for generating primers but also a Python package accessible for integration into various research projects. For those interested in incorporating ExonSurfer into their workflow, the package is available at https://github.com/CrisRu95/ExonSurfer/tree/main. Additionally, the web-tool interface can be built locally using Docker, offering greater flexibility and customization. Detailed instructions and all necessary resources for this setup can be found in the repository at https://github.com/pamonlan/ExonSurferWeb.

If you use ExonSurfer in your research, please cite the following publication:

Monfort-Lanzas, P., Rusu, E.C., Parrakova, L. et al. ExonSurfer: a web-tool to design primers at exon–exon junctions. BMC Genomics 25, 594 (2024). https://doi.org/10.1186/s12864-024-10456-2