The PR2 database
@pr2-database.bsky.social
PR2 is a set of three interconnected sequence public databases focusing on protist taxonomic groups: a reference sequence database (pr2), a primer database (pr2-primers) and a metabarcode database (metapr2).
https://pr2-database.org/
https://pr2-database.org/
Using the PR2 database...
Half of microbial eukaryote literature focuses on only twelve human parasites
#microbiology #protists #eukaryotes
@isme-microbes.bsky.social
academic.oup.com/ismej/articl...
#microbiology #protists #eukaryotes
@isme-microbes.bsky.social
academic.oup.com/ismej/articl...
Half of microbial eukaryote literature focuses on only 12 human parasites
Abstract. Although microbial eukaryotes comprise the majority of eukaryotic phylogenetic diversity and inhabit nearly all ecosystems globally, most researc
academic.oup.com
November 10, 2025 at 6:25 AM
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
Access here: app.pr2-primers.org
Primer database
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<img src="pr2_logo.png" width="80"/>
The PR2 primer database - v. 2.1.0
</div>
app.pr2-primers.org
October 28, 2025 at 9:02 AM
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
Access here: app.pr2-primers.org
Access to the PR2 web interface is here:
app.pr2-database.org
app.pr2-database.org
PR2 databasePR2 reference database
VALIDATE after changes to update screen.
app.pr2-database.org
October 28, 2025 at 8:59 AM
Access to the PR2 web interface is here:
app.pr2-database.org
app.pr2-database.org
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
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
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
doi.org
October 28, 2025 at 8:59 AM
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
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...
Changelog
pr2database.github.io
October 7, 2025 at 8:35 AM
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
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
MetaPR2
app.metapr2.org
October 6, 2025 at 3:28 PM
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
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.
It is an honor to receive the #ISOP Hutner Award to a researcher within 15 years of his PhD who has made outstanding contributions in protistology 😊
I would like to thank my mentors (Ramon Massana, @multicellgenome.bsky.social, @pjkeelinglab.bsky.social) and my past and present students 🙏
I would like to thank my mentors (Ramon Massana, @multicellgenome.bsky.social, @pjkeelinglab.bsky.social) and my past and present students 🙏
June 29, 2025 at 6:57 AM
Javier is the co-coordinaror of PR2... Warn congratulations.
A paper using the PR2 and metaPR2 database.
What’s thriving under Arctic sea ice? We tracked photosynthetic protists during the Arctic UIB,revealing a shift from polar to polar-temperate taxa & spotlighting overlooked groups!Great team & Dr. Sim effort! @biovitenskap.bsky.social @roscoff-collection.bsky.social academic.oup.com/ismecommun/a...
June 28, 2025 at 2:44 PM
A paper using the PR2 and metaPR2 database.
Nice paper making use of PR2
Now published online in Current Biology! www.cell.com/current-biol...
May 7, 2025 at 10:16 AM
Nice paper making use of PR2
Reposted by The PR2 database
@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 👏
April 10, 2025 at 9:01 AM
@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 👏
Reposted by The PR2 database
Grateful I got the opportunity to contribute to this amazing resource #ProtistsOnSky
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:
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:
April 3, 2025 at 1:26 PM
Grateful I got the opportunity to contribute to this amazing resource #ProtistsOnSky
Reposted by The PR2 database
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
- The web interface now provides access to the ROD database that contains full-length eukaryotic ribosomal operons developed by @krabberod.bsky.social
April 3, 2025 at 9:33 PM
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
Please report any issue here:
github.com/vaulot/pr2_d...
github.com/vaulot/pr2_d...
Issues · pr2database/pr2database
Protist Ribosomal Reference database (PR2) - SSU rRNA gene database - Issues · pr2database/pr2database
github.com
April 3, 2025 at 10:53 AM
Please report any issue here:
github.com/vaulot/pr2_d...
github.com/vaulot/pr2_d...
Some functional traits have been added:
- HAB (Harmful Algal Bloom) species
- ecological function - from Sommeria-Klein et al. 2021
- HAB (Harmful Algal Bloom) species
- ecological function - from Sommeria-Klein et al. 2021
April 3, 2025 at 10:53 AM
Some functional traits have been added:
- HAB (Harmful Algal Bloom) species
- ecological function - from Sommeria-Klein et al. 2021
- 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
- Picozoa
- Choropicophyceae
- Rhodophyta
- Dinophyceae
- Foraminifera
April 3, 2025 at 10:53 AM
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
- 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
April 3, 2025 at 10:53 AM
- 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:
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:
April 3, 2025 at 10:53 AM
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:
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:
Please let us know of any problem here: github.com/pr2database/...
Issues · pr2database/pr2database
Protist Ribosomal Reference database (PR2) - SSU rRNA gene database - Issues · pr2database/pr2database
github.com
April 2, 2025 at 2:05 PM
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....
April 2, 2025 at 1:55 PM
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.
April 2, 2025 at 10:59 AM
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...
@amoebadiscovery.bsky.social made an iteresting interview with me about #heliozoa and #centrohelids - I think these organisms are really important, understudied and gorgeous 😍 Also lots other intresting reading and beatiful pictures! #protistsonsky link: tinyurl.com/adiscovery1
March 28, 2025 at 5:40 PM
Protists are not just sequences, they have incredible shapes...
New paper using PR2.
New paper with Norwegian colleagues. Thanks for inviting me to participate... And published by Canadian Science...
cdnsciencepub.com/doi/full/10....
cdnsciencepub.com/doi/full/10....
The community of marine alveolate parasites in the Atlantic inflow to the Arctic Ocean is structured by season, depth, and water mass
The marine alveolates (MALVs) are a highly diverse group of parasitic dinoflagellates, which may regulate populations of a wide range of hosts, including other dinoflagellates, copepods, and fish eggs...
cdnsciencepub.com
March 26, 2025 at 11:14 AM
New paper using PR2.
Looks like a very good tool to use with the PR2 database.
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...
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...
www.biorxiv.org
March 20, 2025 at 8:02 AM
Looks like a very good tool to use with the PR2 database.
Reposted by The PR2 database
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...
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...
www.biorxiv.org
March 19, 2025 at 8:25 AM
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...