The PR2 primer database

version 2.0.0

DOI](https://zenodo.org/badge/latestdoi/437795232)

An interactive database of eukaryotic rRNA primers and primer sets for metabarcoding studies compiled from the literature.

Database structure

  • Primers. Primers have been mapped when possible onto the reference SSU sequence for Saccharomyces cerevisiae (FU970071, 1799 nucleotides, first nucleotide mrearked as 1).

  • Primer sets. Primer sets for 18S rRNA have been tested against the eukaryotic PR2 database version 5.0.0 that contains sequences from Eukaryota, Bacteria, Archaea and Eukaryota plastids. Results can be displayed interactively.

Taxonomy

pr2-primers use a nine-level taxonomy from version 5.0.0 of the PR2 database

One of four “domains” can be selected:

  • Archaea
  • Bacteria
  • Eukaryota
  • Eukaryota:plas - This corresponds to Eukaryota plastid sequences

Panels

  • Primers: table of primers that can be downloaded
  • Primer sets: table of primer sets that can be downloaded
  • Amplification - overview: Give for all primer sets tested % of sequences amplified and amplicon size
  • Amplification - detail: For one primer set tested, detail for different taxonomic levels (kingdom, supergroup, division, class)
  • Test your primer/probe: Test a single primer or probe against PR2 version 4.12.0 and Silva seed 132
  • Test your primer set: Test your primer set against PR2 version 4.12.0 and Silva seed 132
  • About: Basic information on pr2-primers

Errors

Please report errors or primer sets not listed here in the Issues page of the PR2 primer database.

Citation

Vaulot, D., Mahé, F., Bass, D., & Geisen, S. (2021). pr2-primer : An 18S rRNA primer database for protists. Molecular Ecology Resources, in press. DOI: 10.1111/1755-0998.13465

Resources

Maintainer

Contributors to version 1

Versions

2.0.0 - 2023-04-15

  • Use PR2 database version 5.0.0 with 9 levels instead of 8
  • Add 24 primers and 9 primer sets
  • Faster file loading using the qs R library
  • Allow matches to prokaryotes and plastid sequences

1.1.1 - 2022-04-21

  • Run on Google server and not on Docker anymore

1.1.0 - 2021-05-17

  • Panel to test individual primer or probes.
  • Add new primers and primer sets.

1.0.4 - 2021-01-26

  • Add time out of 10 min: after 10 min of inactivity close browser window and stop app.

1.0.2 - 2020-12-25

  • Add non-Metazoa primer and primer sets from Bass and del Campo 2020

1.0.1 - 2020-12-14

  • Fix problem with V9 for bacteria

1.0.0 - 2020-11-11

  • Initial version