The PR2 Database (based on GenBank 203 - October 2014)

The Protist Ribosomal Reference Database provides an access to unicellular eukaryotes Small SubUnit rRNA and rDNA sequences with curated taxonomy. The database is focused on nuclear-encoded sequences of protists. However, Metazoa, land plants and macrosporic fungi, as well as eukaryotic organelles (mitochondrion, plastid and others) are also included because they are useful for Next Generation Sequencing dataset analyses. The PR2 database can be downloaded or searched by similarity as explained below. Because of their tremendous diversity, taxonomy of protists is still under progress.

The PR2 database is updated after each new GenBank Release. Contributions or suggestions are very welcome and can be submitted either to Laure Guillou or to Richard Christen.

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Downloads

    Following downloads are provided :

  • Sequences of the entire database or of any clade (fasta or tabulated files).
  • Amplicon sequences, in silico extracted using commonly used primers (fasta).
  • Phylogenetic trees (Newick format).
  • Representative sequences of each cluster after similarity clustering (fasta).
  • A filter to easily import fasta files in arb.
  • ...

More details given on the Download page.

Search PR2

The PR2 database can be searched as follows :

  • Search by accession number, clade, species ...
  • Local similarities (Blast)
  • Global similarity (Crunch Assign using Needleman-Wunsch)
  • Sequences containing a given primer
  • Clade sequence signatures

More details given on the Search page.

Related pages

The PR2 web site also provide related pages:

  • A list of primers commonly used for PCR (coverage assessed).
  • The putative chimeric sequences we found.
  • A list of descriptive articles, sorted by clade.
  • Introns found in eukaryotic SSU-rRNA gene sequences.
  • PR2 Statistics.
  • ...

More details a given on the Related pages .

Pulpit rock

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