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Protist Ribosomal Reference database (PR2) - SSU rRNA gene database - flat files for mothur

journal contribution
posted on 18.11.2016, 17:28 by Daniel VaulotDaniel Vaulot
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 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.

Files

The files provided are for use with Qiime or Mothur.  Four files are provided.
* pr2....fasta contains all sequences in fasta format
* pr2....tax contains the taxonomy of each sequence
* PR2 version notes.docx contains the revision history
* PR2 versions.xls is a condensed list of the different versions

Current version : 4.4 based on GenBank 203
Last update : 10 nov 2016

Notes
- Qiime can only use 7 taxonomical levels

Contact

Laure GUILLOU and Daniel VAULOT
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.

 


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