Announcing pr2-primers - a new interactive primer database.

The pr2-primers web interface.

We are very pleased to announce the new PR2 primer database.

We built a database listing about 180 primers and 80 primer pairs that have been used for eukaryotic 18S rRNA metabarcoding. Performance of primer pairs was tested against two sequence databases: PR2 for eukaryotes and a subset of Silva for prokaryotes. This allowed to determine the taxonomic specificity of primer pairs, the location of mismatches as well as amplicon size. We developed a R-based web application that allows to browse the database, visualize the taxonomic distribution of the amplified sequences with the number of mismatches, and to test any user-defined primer set.

Maintainer

  • Daniel Vaulot: vaulot@gmail.com

Contributors

  • Stefan Geisen: stefan.geisen@wur.nl
  • Fréderic Mahé: frederic.mahe@cirad.fr
  • David Bass: david.bass@cefas.co.uk

Citation

Vaulot D., Geisen S., Mahé F., Bass D. 2020. pr2-primers: an 18S rRNA primer database for protists. Methods in Ecology and Evolution submitted to Molecular Ecology Resources, deposited to BioRxiv.

Avatar
Daniel Vaulot
NTU, Singapore

Focusing on marine (pico)phytoplankton .

Related