Protist Ribosomal Reference database (PR2) - SSU rRNA gene database
The original web site (http://ssu-rrna.org/pr2) is currently out and we are proposing updated version of PR2 as flat files to use for annotating metabarcodes.
Current version : 4.62 (version 15 on Figshare)
Last update : 11 September 2017
- pr2_version_4.x_mothur.zip contains two files for use with Qiime or Mothur.
* pr2....fasta contains all sequences in fasta format with the accession in the description line
* pr2....tax contains the taxonomy of each sequence separated from the accession number by a tabulation
- pr2_version_4.x_taxo_long.zip contains one fasta file with the accession number of the sequence, the name of the sequence and its full taxonomy on the description line. It is suitable to build a local database for BLAST search
- PR2 version notes.docx contains the revision history
- PR2 versions.xls is a condensed list of the different versions
- Qiime only use 7 taxonomical levels by default.
Daniel VAULOT, Laure GUILLOU and Fabrice NOT
DIPO team, Plankton Group, UMR 7144 CNRS-UPMC
Place G. Tessier
29680 Roscoff FRANCE
- Tristan Biard
- Margot Tragin
- Bente Edvardsen
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.
Edvardsen, B., Egge, E.S. & Vaulot, D. 2016. Diversity and distribution of haptophytes revealed by environmental sequencing and metabarcoding – a review. Perspect. Phycol. in press
Tragin, M., Lopes dos Santos, A., Christen, R. & Vaulot, D. 2016. Diversity and ecology of green microalgae in marine systems: an overview based on 18S rRNA gene sequences. Perspect. Phycol. in press.
Note : The PhytoRef (16S plastid database) is available here : https://figshare.com/articles/PhytoREF_a_reference_database_of_the_plastidial_16S_rRNA_gene_of_photosynthetic_eukaryotes_with_curated_taxonomy/4689826