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Protist Ribosomal Reference database (PR²)

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SSU rRNA gene database

The PR² database was initiated in 2010 in the frame of the BioMarks project from work that had developed in the previous ten years in the Plankton Group of the Station Biologique of Roscoff. Its aim is to provide a reference database of carefully annotated 18S rRNA sequences using eight unique taxonomic fields (from domain to species). At present it contains about 240,000 sequences. A number of metadata fields are available for many sequences, including geo-localisation, whether it originates from a culture or a natural sample, host type etc… The annotation of PR2 is performed by experts from each taxonomic groups. One very important project in this respect is EukRef which has recently decided to merge its effort with PR². EukRef has built bioinformatics pipelines that have been used during three workshops dedicated to specific taxonomic groups.

The web interface now includes links to the sequences of the Ribosomal Operon Database (ROD) published in Krabberød, A.K., Stokke, E., Thoen, E., Skrede, I. & Kauserud, H. 2025. The Ribosomal Operon Database: A Full-Length rDNA Operon Database Derived From Genome Assemblies. Molecular Ecology Resources. 25:e14031) and to the eKOI database which is a curated COI gene database .

Current version

• Version: 5.1.2

• Released: 2026-02-22

• DOI:

Accessing PR2

On the web

1. Flat files - latest release
2. Web interface

On your computer

1. Run as docker container. <= This is the best way
2. R package

1 - Docker container (Easier)

Available from Docker repository

• Install docker on your computer: https://docs.docker.com/desktop/

• At shell prompt (can be Linux, Mac or Windows Powershell). Note that a Powershell window can be opened from RStudio Terminal or VSCode Terminal.

# Download container
docker pull vaulot/pr2-database:latest

# Launch container
docker run --rm -p 8080:8080 vaulot/pr2-database

• In your browser: http://localhost:8080/
• To exit type CTRL-C in the shell prompt

2 - Installing and running PR2 as a R package (Hard way)

• Requires R version 4.4.
• You may have to install some packages required by pr2database if they are not installed on your machine.

<!-- -->

# Installing necessary packages

install.packages("devtools")
install.packages("remotes")

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

remotes::install_version("blaster", version = "1.0.7")

BiocManager::install("Biostrings")

install.packages("devtools")
devtools::install_github("pr2database/pr2database")

# Run the shiny application
pr2database::run_app()

About PR2

• Documentation
• Statistics

Core Team

• Daniel VAULOT, Station Biologique de Roscoff, CNRS, France and University of Oslo, Norway
• Javier del CAMPO, Institut de Biologia Evolutiva, Barcelona, Spain

Scientific committee and contributors

• PR² team

Please cite

• Guillou, L., Bachar, D., Audic, S., Bass, D., Berney, C., Bittner, L., Boutte, C. et al. 2013. The Protist Ribosomal Reference database (PR²): a catalog of unicellular eukaryote Small Sub-Unit rRNA sequences with curated taxonomy. Nucleic Acids Res. 41:D597–604.

Related Projects

18S rRNA primer database

The PR² primer database is a compilation of primers found in the litterature with an in silico analysis against the PR² database.

metaPR2

The metaPR² metabarcode database is a compilation of metabarcode datasets processed by the dada2 R package and assigned against PR2.

Ribosomal Operon Database (ROD) - version 1.2

The ROD database contains full-length eukaryotic ribosomal operons. The database is based on the genome assemblies from NCBI, and the operons are extracted from the assemblies. The database currently contains 69,480 operon variants from more than 11,935 genomes.

Eukaryotic mitochondrial cytochrome oxidase (coi) Database (eKOI) - version 1.0

The eKOI database is a curated COI gene database designed to enhance the taxonomic annotation for protists that can be used for COI-based metabarcoding. eKOI integrates data from GenBank and mitochondrial genomes, followed by extensive manual curation to eliminate redundancies and contaminants, recovering 15 947 sequences within 80 eukaryotic phyla.

Questions ?

• Register to our element.io discussion board

Report issues

• Please report any issue on GitHub