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title Primerool: Project Features & Workflow
author Mgr. Vojtěch Rejtar
date 2026-02-24

Primerool: Project Overview

Author: Mgr. Vojtěch Rejtar Date: February 24, 2026 Project: Primerool

Primerool is a cloud-based, local web application that allows molecular biologists to search for genes, visualise their genomic structure, and design PCR primers directly from the browser, fetching live data from Ensembl and NCBI.

Features and Capabilities

  1. Gene Search & Sequence Retrieval

    • Live querying of Ensembl or NCBI by gene name (e.g., BRCA1) or accession ID.
    • Retrieves all annotated transcripts, canonical transcript auto-selection, full genomic DNA, spliced mRNA, UTRs, and configurable flanking regions.

  2. Multi-Organism Support

    • Support for 6 kingdoms (Animals, Plants, Bacteria, Fungi, Protists, Viruses) and over 40 pre-configured species.
    • Custom Ensembl species identifier support.

  3. Dual Data Source

    • Ensembl REST API natively supported.
    • NCBI E-Utilities as a robust, native fallback.

  4. BLAST Integration

    • FASTA mode to run NCBI BLAST sequence searches.
    • Auto-fills the gene search with the matched organism and gene from top hits.

  5. Interactive Sequence Visualisation

    • Feature Map: Zoomable timeline showing exons, introns, CDS, and UTRs.
    • Sequence Map: Full nucleotide sequence with colour-coded annotations, primer binding site highlights, and interactive navigation between features.

  6. Five Primer Design Modes

    • WGA (Whole-Genome Amplification): Primers in flanking regions for amplifying the entire locus. Relaxed GC% (20–80%) and Tm (52–68°C) for AT/GC-rich genomic regions.
    • Internal (Exon-Exon Junction): Splice-spanning primers for qRT-PCR, with configurable junction overlap (default 6–12 bp) and product size (default 80–220 bp).
    • Design from Sequence (Manual): Targeting specific user-provided forward and reverse regions. Supports target amplicon length with a configurable deviation (default ±50 bp), constraining the picker to products of the desired size.
    • Probe Design (TaqMan): Design internal oligos (hydrolysis probes) from any sequence region. Configurable probe Tm (default 65/70/75°C min/opt/max), length (default 18/22/30 bp), and GC% (default 30–80%). Each probe is reported with Tm, GC%, hairpin ΔG, and homodimer ΔG.
    • Automatic Pairing: Configurable conditions (Tm, Length, GC%) applied across all primer modes, with heterodimer cross-check for each returned pair.

  7. Quality Control

    • Real-time thermodynamic checking for hairpin formation, self-dimer (homodimer), and heterodimer cross-complementarity computed by the native Strider engine.

Typical Workflow

  1. Launch the Application

    • Use the hosted app, or run it locally with npm run setup && npm run dev (see the README's Quick start).
    • For a native desktop window, build the Tauri shell: cargo tauri build.

  2. Organism and Data Source Selection

    • Select your target organism and preferred data API (Ensembl or NCBI).

  3. Search for Target Gene

    • Enter a gene symbol (e.g., BRCA1) or use the FASTA mode / BLAST integration to identify a target sequence.
    • Primerool fetches the gene's structure and canonical transcript automatically.

  4. Prepare Sequence for Design

    • Uncheck or check visual elements like Introns or UTRs based on your needs.
    • Configure the upstream and downstream flanking regions.

  5. Review Genomic Structure

    • Use the Feature Map to get a high-level view of exon layouts.
    • Scroll through the Sequence Map to analyze specific sequence ranges.

  6. Design Primers

    • Select a primer design mode (e.g., Exon-Exon Junction for expression profiling, Manual design with a target amplicon length, or Probe Design for TaqMan assays).
    • Adjust primer conditions like Tm, GC%, and amplicon size as needed.
    • For probe design, paste a sequence region and configure probe Tm, length, and GC% in the Probe Conditions panel.
    • Click "Design Primers" or "Design Probe" and review the ranked results alongside their QC stats (Tm, GC%, hairpins, dimers, heterodimers).
    • Click "Use" on a primer pair to visually highlight their exact binding sites on the Sequence Map.