The PR2 primer database

A database of eukaryotic rRNA primers and primer sets for metabarcoding studies compiled from the literature.

Primers

column definition
primer_id primer id in pr2-primers database
name original name of the primer
synonyms synonyms found in the litterature
sequence
sequence revcomp reverse complement of the sequence
direction forward (fwd) or reverse (rev)
start_yeast start of primer relative to FU970071
end_yeast end of primer relative to FU970071
specificity is the primer specific of a group
reference original reference where primer was first defined
doi link to original paper

Download primers

Primer sets

(see Primers table for other fields)

column definition
region gene region targetted. Universal corresponds to primer sets that amplify both prokaryotes and eukaryotes
specificity is the primer specific of a group
primer_set_id id of the primer set in pr2-primers database
primer_set_name name of the primer set (usually from author)
fwd/rev_name forward/reverse primer name
fwd/rev_seq forward/reverse primer sequence
fwd/rev_start start of primer relative to FU970071
fwd/rev_end end of primer relative to FU970071
length length of amplified sequence relative to FU970071
reference original reference where primer set was first defined
doi link to original paper

Download primer sets

Precomputed results for primer sets

Against PR2 sequence database

Precomputed results for primer sets

Against PR2 sequence database

Test your primer set

Primer set is tested against the PR2 database.

Use only UIPAC characters ( ACGTRYSWKMBDHVN ).

Length of primers: between 15 and 30 bp.


The PR2 primer database


DOI

An interactive database of eukaryotic rRNA primers and primer sets for metabarcoding studies compiled from the literature.

Database structure

Panels

  • About: Basic information
  • Primers: table with download
  • Primer sets: table with download
  • Amplification - overview: Give for all primer sets tested % of sequences amplified and amplicon size
  • Amplification - detail: For one primer set tested, detail for different taxonomic levels (kingdom, supergroup, division, class)
  • Test your own: Test your primers against PR2 version 4.12.0 and Silva seed 132

Errors

Please report errors or primer sets not listed here in the Issues page of the PR2 primer database.

Citation

Vaulot D., Geisen S., Mahé F., Bass D. 2020. pr2-primers: an 18S rRNA primer database for protists. Methods in Ecology and Evolution submitted. deposited to BioRxiv.

Resources

Maintainer

Contributors

Versions

1.0.4 - 2021-01-26

  • Add time out of 10 min: after 10 min of inactivity close browser window and stop app.

1.0.2 - 2020-12-25

  • Add non-Metazoa primer and primer sets from Bass and del Campo 2020

1.0.1 - 2020-12-14

  • Fix problem with V9 for bacteria

1.0.0 - 2020-11-11

  • Initial version
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