Protist Ribosomal Reference database (PR2)
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 : 4.11.1
- Last update : 13 December 2018
- DOI : https://doi.org/10.6084/m9.figshare.5913181
- Manual : https://github.com/pr2database/pr2database/wiki
Downloading the database
R package using Devtools
- Please report any issue on GitHub
- 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
- 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 Sites and databases
Eukref (18S annotation)
PhytoRef (16S plastid)
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”.