The PR2 database

Using Docker for work? We recommend signing in with your work email address.

For those of you who are using metaPR2 extensively, a good alternative to installing the R package which can cause trouble because of dependencies, you can try the newly available docker container:
hub.docker.com/repository/d...

Rare microbial relict sheds light on an ancient eukaryotic supergroup - Nature The discovery of an unusual protist named Solarion arienae, which has a mitochondrial genome with some intriguing features, provides insight into the early radiation of eukaryotic groups.

Using PR2

www.nature.com/articles/s41...

Using the PR2 database...

PR2 primers version 2.1.0 has been released. This does not include any new primer, but now the database uses the latest version of PR2 (5.1.1) to perform in silico analyses.
Access here: app.pr2-primers.org

PR2 databasePR2 reference database VALIDATE after changes to update screen.

Access to the PR2 web interface is here:
app.pr2-database.org

A novel taxonomic database for eukaryotic mitochondrial cytochrome oxidase subunit I gene (eKOI), with a focus on protists diversity Abstract. Metabarcoding has emerged as a robust method for assessing biodiversity patterns by retrieving environmental DNA directly from ecosystems. While

Version 5.1.1 of the PR2 database has been released.

The major novelty is the inclusion of the recently published eKOI database (coi gene- doi.org/10.1093/data...) in the web interface. The 18S rRNA database is not changed so you can use 5.1.0 or 5.1.1 for metabarcode annotations

More info here: pr2database.github.io/metapr2-shin...

metaPR2 version 3.0 has just been released.

Here are the major changes:
- Metabarcodes (ASVs) are now annotated with the latest version of the PR2 reference sequence database (5.1.0).
- 8 new published datasets have been added from the Arctic and from the South West Pacific.

app.metapr2.org

Javier is the co-coordinaror of PR2... Warn congratulations.

A paper using the PR2 and metaPR2 database.

Nice paper making use of PR2

@daniel-vaulot.bsky.social presenting the @pr2-database.bsky.social at our DNA metabarcoding course at @biovitenskap.bsky.social A very good new addition to our biannual course 👏

Grateful I got the opportunity to contribute to this amazing resource #ProtistsOnSky

I am very happy that ROD (The Ribosomal Operon Database) is now included in the outstanding PR2 web interface, enhancing its accessibility and utility. I hope to make some updates to ROD in the near future. with @drhyfe.bsky.social

Issues · pr2database/pr2database Protist Ribosomal Reference database (PR2) - SSU rRNA gene database - Issues · pr2database/pr2database

Please report any issue here:
github.com/vaulot/pr2_d...

Some functional traits have been added:

- HAB (Harmful Algal Bloom) species
- ecological function - from Sommeria-Klein et al. 2021

A few taxonomic groups have been updated from work performed during the 2023 Barcelona EukRef workshop and from individual contributions including:

- Picozoa
- Choropicophyceae
- Rhodophyta
- Dinophyceae
- Foraminifera

- The web interface now provides access to the ROD database that contains full-length eukaryotic ribosomal operons developed by @krabberod.bsky.social

Announcing the new release of the PR2 database, version 5.1.
pr2-database.org/post/news/20...

Very big thanks to all the contributors: @fonamental.bsky.social @ambonacolta.bsky.social @krabberod.bsky.social and more...

A few highlights:

Issues · pr2database/pr2database Protist Ribosomal Reference database (PR2) - SSU rRNA gene database - Issues · pr2database/pr2database

Please let us know of any problem here: github.com/pr2database/...

We are back on-line. It took less time than anticipated to upgrade R....

The PR2, metaPR2 and PR2-primers websites will be off in the coming days as we are switching from R 3.6 to R 4.4.

Protists are not just sequences, they have incredible shapes...

New paper using PR2.

Looks like a very good tool to use with the PR2 database.

raxtax: A k-mer-based non-Bayesian Taxonomic Classifier Taxonomic classification in biodiversity studies is the process of assigning the anonymous sequences of a marker gene (barcode) to a specific lineage using a reference database that contains named seq...

Check out raxtax, our new open-source tool for taxonomic classification of barcoding sequences, it's 2.7-1000 times faster than competing tools and also implements fancy uncertainty scores: www.biorxiv.org/content/10.1...

A tool to use with the metaPR2 datasets ?

All PR2 shiny servers are back up and running...

From the Richter lab in Barcelona... new species are always exciting...

Join a world renowned marine lab in France.

New Junior Professor Chair (CPJ) opened in the Biological Station in Roscoff. The position is focused on the ecological, evolutionary, and functional roles of marine fungi, crucial to understanding our oceans.

www.sb-roscoff.fr/fr/2025/02/2...