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Protist Ribosomal Reference database (PR2) - SSU rRNA gene database
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README.md

Protist Ribosomal Reference database (PR2)

Release Date Github Downloads (total) Twitter URL

SSU rRNA gene database

The Protist Ribosomal Reference database (PR2) provides a unique access to eukaryotic small sub-unit (SSU) ribosomal RNA and DNA sequences, with curated taxonomy. The database mainly consists of nuclear-encoded protistan sequences. However, metazoans, land plants, macrosporic fungi are also included because they are useful for the analysis of high-troughput sequencing data sets. Introns and putative chimeric sequences have been also carefully checked. Taxonomic assignation of sequences consists of eight unique taxonomic fields.

Since the original web site (http://ssu-rrna.org/pr2) does not exist any more, we are proposing updated version of PR2 and provide the data in a variety of file formats to use for annotating metabarcodes.

Current version

Downloading the database

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

Basic statistics

Report issues

  • Please report any issue on GitHub

Contact

Daniel VAULOT, Laure GUILLOU and Fabrice NOT, ECOMAP team, Plankton Group, UMR 7144 CNRS-UPMC Station Biologique, Place G. Tessier 29680 Roscoff FRANCE email: vaulot@sb-roscoff.fr / vaulot@gmail.com

Contributors

  • Tristan Biard (Wimereux Station)
  • Margot Tragin (Roscoff)
  • Bente Edvardsen (U of Oslo)
  • Charles Bachy and Wei Ting Chen (Roscoff)
  • Solenn Mordret (Naples)
  • Adriana Lopes dos Santos (Nanyang Technological University, Singapore)
  • Vittorio Boscaro (UBC, Vancouver) and the EukRef ciliate team

Please cite

Related Sites and databases

Eukref (18S annotation)

PR2 will be incorporating annotations made by the EukRef project as deposited in their GitHub repository.

PhytoRef (16S plastid)

Plastid 16S rRNA sequences are yet not included into PR2. These sequences are available from the the PhytoRef database available from Figshare or PhytoRef.

PFR2 - Foraminifera 18S ribosomal DNA databae

The database offers access to planktonic Foraminifera 18S ribosomal DNA sequence library with a curated taxonomy at the morphological and molecular level. The compilation was facilitated through the efforts of the SCOR/IGBP Working Group 138 “Modern planktonic foraminifera and ocean changes”.

PFR2

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