Major update of the metaPR2 database with 120 new datasets and more than 18,000 samples. pr2-database.org/post/news/20...
metaPR2 version 4.0.0 | The PR2 databases
Adding 120 datasets to the database.
pr2-database.org
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/
New article on #protist global distributions combining the #Mixoplankton and #metaPR2 databases with revised functional annotations led by @lusantof.bsky.social, Michaela E. Larsson, and Suzana Leles with Aditee Mitra and Emile Faure. Now available on Ocean Microbiology rdcu.be/fanlx
Docker containers are now available for the three PR2 applications: - pr2-database: reférence database - pr2-primers: primer database and analysis - metapr2: metabarcode database and visualization. This by far the easiest way to use these databases on your computer. hub.docker.com/repositories...
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...
Using Docker for work? We recommend signing in with your work email address.
hub.docker.com
Using PR2 www.nature.com/articles/s41...
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.
nature.com
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
Primer database <div> <img src="pr2_logo.png" width="80"/> The PR2 primer database - v. 2.1.0 </div>
app.pr2-primers.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
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
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
MetaPR2
app.metapr2.org
Javier is the co-coordinaror of PR2... Warn congratulations.
Javier del Campo@fonamental.bsky.social · last yr.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 🙏
A paper using the PR2 and metaPR2 database.
Adriana Lopes@lopessantosadriana.bsky.social · last yr.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...
@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
The PR2 database@pr2-database.bsky.social · last yr.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:
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 PR2 database@pr2-database.bsky.social · last yr.- 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:
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...
Vasily Zlatogursky@zlatogursky.bsky.social · last yr.@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
Looks like a very good tool to use with the PR2 database.
Alexis Stamatakis@stamatak.bsky.social · last yr.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...
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...
biorxiv.org
A tool to use with the metaPR2 datasets ?
Amy D Willis@amydwillis.bsky.social · last yr.We've just released radEmu v2.0.0 🥳🦤😻 `remotes::install_github("statdivlab/radEmu")` A huge thanks to users for sharing their requests and questions, and to the maintenance team (Sarah and @davidandacat.bsky.social ) for their time and commitment! Release notes: github.com/statdivlab/r...
All PR2 shiny servers are back up and running...
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...
Open position Junior Professor Chair (CPJ)
Open position Junior Professor Chair (CPJ) 2025. CNRS EE-BIO
sb-roscoff.fr
Very interesting paper #usingPR2
Kenneth Dumack@dumack.bsky.social · last yr.Have you used #network_analyses in the past to analyse your #ecology data? Have you wondered how many of those correlations actually represent interactions between #microorganisms? Here I present a paper how we leveraged #protistsonsky to evaluate the validity of the method. A thread:
Registration is now open for the ForBio/UiO course “Bioinformatics for environmental DNA sequencing” @biovitenskap.bsky.social @drhyfe.bsky.social @krabberod.bsky.social @ramalok.bsky.social www.forbio.uio.no/events/cours...
ForBio and UiO/IBV course: Bioinformatics for environmental DNA sequencing - ForBio
Read this story on the University of Oslo's website.
forbio.uio.no
This very interesting Nature paper uses the metaPR2 database to assess the distribution of DPH containing diatoms.
Angela Falciatore@afalciat.bsky.social · 2y agoExcited to share this work from our lab @IBPC and collaborators! Thanks to diatoms, some of the mysteries surrounding phytochrome photoreceptors in the oceans are beginning to be unraveled! Phytochrome remains the "pigment of imagination’ Congratulations to all the authors! doi.org/10.1038/s415...
A new #StarterPack with scientist specialized in microbial bioinformatics - #MicroBioInf. Please comment if you would like to be added: go.bsky.app/5h7VaGm Looking forward to the discussions!
#usingpr2 www.sciencedirect.com/science/arti...
Indications of a benthic foraminifer Cribrononion gnythosuturatum to salinities revealed by eDNA metabarcoding and morphological methods
Cribrononion gnythosuturatum is a widely distributed benthic foraminifer. However, its adaptability to salinity changes is still poorly understood. To…
sciencedirect.com