PR2

PR2 provides a curated database of eukaryotic 18S rRNA primers and evaluates their in silico performance to guide primer selection for protist metabarcoding.

Key Features:

• Extensive Primer Database: Contains 179 individual primers and 76 primer pairs curated from the literature for eukaryotic 18S rRNA metabarcoding.
• In silico Performance Testing: Evaluates primers against the PR2 eukaryotic sequence database and a subset of Silva for prokaryotes to determine taxonomic specificity, mismatches, and amplicon sizes.
• Custom Primer Testing: Supports in silico testing of user-specified primer sets and reports mismatch occurrences and expected amplicon size distributions.
• Taxonomic Distribution Analysis: Reports the taxonomic distribution of sequences predicted to be amplified by each primer or primer pair.

Scientific Applications:

• Primer selection for protist metabarcoding: Informs choice of 18S rRNA primers to improve coverage and representation of protist communities.
• Assessment of primer specificity: Identifies potential off-target amplification, including detection of prokaryotic matches via the Silva subset.
• Optimization of amplicon design: Evaluates expected amplicon sizes and mismatch patterns to inform experimental primer design decisions.

Methodology:

Primers were compiled from the literature and subjected to in silico testing against the PR2 eukaryotic database and a subset of Silva to assess taxonomic specificity, mismatches, and amplicon sizes.