DATASET
PR2 versions.xlsx (27.24 kB)
DOCUMENT
PR2 version notes.docx (21.76 kB)
ARCHIVE
pr2_version_4.62_mothur.zip (69.28 MB)
ARCHIVE
pr2_version_4.62_taxo_long_Eukaryota.zip (72.88 MB)
ARCHIVE
pr2_version_4.62_UTAX.zip (71.88 MB)
ARCHIVE
pr2_version_4.62_metadata.zip (9.72 MB)
1/0
Protist Ribosomal Reference database (PR2) - SSU rRNA gene database
Version 19 2018-02-21, 21:10
Version 18 2017-11-21, 19:10
Version 17 2017-10-07, 15:25
Version 16 2017-09-27, 11:48
Version 15 2017-09-11, 12:37
Version 14 2017-09-08, 17:01
Version 13 2017-09-06, 09:37
Version 12 2017-08-25, 11:48
Version 11 2017-01-20, 19:04
Version 10 2017-01-17, 12:46
Version 9 2017-01-17, 12:42
Version 8 2017-01-17, 12:06
Version 7 2017-01-17, 12:03
Version 6 2016-11-18, 17:28
Version 5 2016-11-18, 17:14
Version 4 2016-09-04, 09:46
Version 3 2016-09-04, 09:32
Version 2 2016-09-03, 12:41
Version 1 2016-09-02, 15:54
dataset
posted on 2017-09-11, 12:37 authored by Daniel VaulotDaniel VaulotThe 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
and eukaryotic
organelles (mitochondrion, plastid and others) 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.
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
Files
- 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
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
Files
- 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_UTAX.zip contains one fasta file with the accession number of the sequence and its full taxonomy on the description line in the UTAX format. It is suitable to use with USEARCH and VSEARCH.
- 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_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_4.x_metadata.zip contains a tabulation separated file with all the metadata from genbank as well as annotation made to the PR2 database.
- PR2 version notes.docx contains the revision history
- PR2 versions.xls is a condensed list of the different versions
Notes
- Qiime only use 7 taxonomical levels by default.
Contact
Daniel VAULOT, Laure GUILLOU and Fabrice NOT
DIPO team, Plankton Group, UMR 7144 CNRS-UPMC
Station Biologique,
Place G. Tessier
29680 Roscoff FRANCE
email: vaulot@sb-roscoff.fr
Contributors
- Tristan Biard
- Margot Tragin
- Bente Edvardsen
References
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
- PR2 version notes.docx contains the revision history
- PR2 versions.xls is a condensed list of the different versions
Notes
- Qiime only use 7 taxonomical levels by default.
Contact
Daniel VAULOT, Laure GUILLOU and Fabrice NOT
DIPO team, Plankton Group, UMR 7144 CNRS-UPMC
Station Biologique,
Place G. Tessier
29680 Roscoff FRANCE
email: vaulot@sb-roscoff.fr
Contributors
- Tristan Biard
- Margot Tragin
- Bente Edvardsen
References
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
History
Usage metrics
Categories
- Phycology (incl. marine grasses)
- Marine and estuarine ecology (incl. marine ichthyology)
- Biogeography and phylogeography
- Plant cell and molecular biology
- Animal cell and molecular biology
- Bioinformatics and computational biology not elsewhere classified
- Microbial ecology
- Microbiology not elsewhere classified
Keywords
Licence
Exports
RefWorks
BibTeX
Ref. manager
Endnote
DataCite
NLM
DC