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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. Four Primer Design Modes

    • WGA (Whole-Genome Amplification): Primers in flanking regions for amplifying the entire locus.
    • Internal (Exon-Exon Junction): Splice-spanning primers for qRT-PCR.
    • Design from Sequence (Manual): Targeting specific user-provided forward and reverse regions.
    • Automatic Pairing: Configurable conditions (Tm, Length, GC%).

  7. Quality Control

    • Real-time thermodynamic checking for hairpin formation, self-dimer (homodimer), and heterodimer cross-complementarity using Primer3 engine precision.

Typical Workflow

  1. Launch the Application

    • macOS: Open the Primerool.app bundle to launch the native desktop application.
    • Windows: Run Run_primerool.bat or Primerool.exe to start the application.

  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, or Manual design).
    • Adjust primer conditions like Tm and GC% if needed.
    • Click "Design Primers" and review the ranked primer pairs alongside their QC stats (hairpins, dimers).
    • Click "Use" on a pair to visually highlight their exact binding sites on the Sequence Map.