GRACE is a standalone, offline, cross‑platform desktop application for microsatellite (SSR) marker development. It combines SSR detection, Primer3‑based primer design, BLAST specificity filtering, genomic annotation, and lab‑ready exports in a single graphical interface — no command line needed.
- SSR Detection – fast regex‑based scanning for di‑ to hexanucleotide repeats, with canonical motif standardisation and optional adjacent‑motif filtering.
- SSR Summary – interactive karyotype view showing SSR positions along chromosomes, motif type distribution, and genomic feature breakdown (exon/intron/intergenic) when a GFF is loaded.
- Primer Design – Primer3‑powered design with quality filters. Two parameter presets:
- Capillary Electrophoresis – optimised for fragment analysis (M13 tails, dye multiplexing).
- Amplicon Sequencing – optimised for Illumina amplicon panels (P5/P7 tails, tight Tm, short products).
- Specificity Checking – bundled BLAST+ binaries; no external installation required.
- GFF Annotation – optional GFF3/GTF support for exon/intron/intergenic classification and chromosome name mapping.
- Three Complete Workflows
- Amplicon Sequencing – validate multiplex primer pools for dimer risks, amplicon size, and GC content. Optimise panels and export tailed primers with amplicon reference sequences.
- Capillary Electrophoresis – assign dyes (FAM, VIC, NED, PET) and size bins. Supports multiple panels (injections) and exports ready‑to‑order primers with M13 tails.
- GBS‑RE (Restriction‑Enzyme GBS) – discover SSRs located within user‑defined restriction fragments (e.g. PstI‑MspI). Compare enzyme combinations, generate barcodes, and export marker lists.
- Linkage Disequilibrium Filter – thin markers by physical distance across all workflows.
- Chromosome View – visualise marker positions on chromosomes or contigs throughout the application.
- Project Summary – dynamic, tabbed summary of all completed steps with embedded charts. Export a comprehensive PDF report.
Download the latest release for your platform from the Releases page. Extract the folder and run GRACE.exe (Windows) or open GRACE.app (macOS). BLAST+ is bundled – no separate installation required.
git clone https://github.com/jackburton-qub/GRACE.git
cd GRACE
pip install -r requirements.txt
python main.py
Workflow
text
01 Load Genome – FASTA/FASTQ + optional GFF3/GTF annotation
02 Detect SSRs – scan for perfect repeats, annotate with genomic features
03 SSR Summary – visualise distribution and statistics
04 Design Primers – Capillary or Amplicon Sequencing mode
05 Check Specificity – BLAST primers against the genome
06 BLAST Results – review and filter by specificity
07 Project Summary – complete pipeline overview with PDF export
08 Amplicon Tools – multiplex validation and panel optimisation
09 Capillary Tools – dye assignment and size binning
10 GBS‑RE Tools – restriction fragment marker discovery
Dependencies
Package Purpose
PyQt6 Desktop GUI framework
primer3‑py Primer design
pandas Data handling
numpy Numerical operations
reportlab PDF report generation
BLAST+ Bundled – specificity checking
Supported File Formats
Format Input Output
FASTA (.fa, .fasta, .fna) ✓
FASTQ (.fastq, .fq) ✓
GenBank (.gb, .gbff, .gbk) ✓
GFF3 (.gff, .gff3) ✓
GTF (.gtf) ✓
CSV ✓
FASTA (primers, amplicons) ✓
PDF ✓
JSON (session) ✓ ✓
Licence
MIT – see LICENSE for details.