pr2-primers

pr2-primers provides a curated database and in silico performance evaluations of primers targeting the eukaryotic 18S rRNA gene to inform primer selection for microbial eukaryote (protist) metabarcoding studies.

Key Features:

• Extensive primer collection: Compiles 285 individual primers and 83 unique primer pairs specifically used to amplify the eukaryotic 18S rRNA gene.
• In silico performance testing: Evaluates primer and primer-pair performance against PR^2 version 4.12.0 for eukaryotes and a subset of Silva version 132 for bacteria and archaea.
• Taxonomic specificity analysis: Reports taxonomic distributions of amplified sequences and assesses taxon-level specificity of primer pairs.
• Amplicon size and mismatch analysis: Predicts amplicon sizes and identifies locations and numbers of mismatches between primers and reference sequences.
• Universal primer identification: Identifies primer sets that match a large fraction of reference sequences for broad-spectrum protist surveys.
• User-defined primer evaluation: Supports assessment of mismatches and predicted amplification for user-specified primers or primer sets.

Scientific Applications:

• Metabarcoding primer selection: Informs selection of 18S rRNA primer pairs for microbial eukaryote (protist) metabarcoding studies.
• Assessment of primer coverage and bias: Enables evaluation of taxonomic coverage and potential biases introduced by specific primers or primer pairs.
• Non-target amplification assessment: Allows checking of primer specificity against bacterial and archaeal sequences using a Silva v132 subset to reduce non-target amplification.
• Design of broad or targeted surveys: Facilitates identification of universal primer sets for broad community surveys or primers targeting specific protist groups.

Methodology:

Primer sequences were compiled from the literature and subjected to in silico performance testing against PR^2 version 4.12.0 and a subset of Silva version 132 to evaluate mismatches and predicted amplicon sizes.