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

2017-01-20T19:04:45Z (GMT) by Daniel Vaulot
The Protist Ribosomal Reference database (PR<sup>2</sup>) 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.<br><br>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.<br><br><b>Files</b><br><br><b>- pr2_gb203_version_4.x.zip</b> contains two files for use with Qiime or Mothur.<br>   * <b>pr2....fasta</b> contains all sequences in fasta format with the accession in the description line<br>   * <b>pr2....tax</b> contains the taxonomy of each sequence separated from the accession number by a tabulation<br><br><b>- pr2_gb203_version_4.x.for_BLAST.zip</b> contains one fasta file with the accession number of the sequence and its taxonomy on the description line.  It is suitable to build a local database for BLAST search<br><br>- <b>PR2 version notes.docx</b> contains the revision history<br><br>- <b>PR2 versions.xls</b> is a condensed list of the different versions<br><br><b>Current version</b> : 4.5 based on GenBank 203<br><b>Last update</b> : 17 January 2017<br><br><b>Notes<br></b>- Qiime can only use 7 taxonomical levels<b><br><br>Contact<br><br></b>Laure GUILLOU and Daniel VAULOT<br>DIPO team, Plankton Group, UMR 7144 CNRS-UPMC<br>Station Biologique,<br>Place G. Tessier<br>29680 Roscoff FRANCE<br>email: vaulot@sb-roscoff.fr<br><br><b>Contributors<br><br></b>- Tristan Biard<br>- Margot Tragin<br>- Bente Edvardsen<br> <br><b>References</b><br><p>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. <i>Nucleic Acids Res.</i> 41:D597–604.</p><p>Edvardsen, B., Egge, E.S. & Vaulot, D. 2016. Diversity and distribution of haptophytes revealed by environmental sequencing and metabarcoding – a review. <i>Perspect. Phycol.</i> in press.</p><p>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. <i>Perspect. Phycol.</i> in press.</p> <br><br><br>