https://github.com/jackburton-qub/grace

Genomic Repeat Analysis and Characterisation Engine
https://github.com/jackburton-qub/grace

bioinformatics blast blastn microsatellite primer-design pyqt6 ssr

Last synced: 2 months ago
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Genomic Repeat Analysis and Characterisation Engine

• Host: GitHub
• URL: https://github.com/jackburton-qub/grace
• Owner: jackburton-qub
• License: mit
• Created: 2026-03-20T16:09:06.000Z (4 months ago)
• Default Branch: master
• Last Pushed: 2026-04-16T15:50:41.000Z (3 months ago)
• Last Synced: 2026-04-16T17:21:34.999Z (3 months ago)
• Topics: bioinformatics, blast, blastn, microsatellite, primer-design, pyqt6, ssr
• Language: Python
• Homepage:
• Size: 1.49 MB
• Stars: 0
• Watchers: 0
• Forks: 0
• Open Issues: 0
• Metadata Files:
  • Readme: README.md
  • License: LICENSE
  • Citation: CITATION.cff

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README

          
# GRACE

### Genomic Repeat Analysis and Characterisation Engine

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.

---

## Features

- **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.

---

## Installation

### Pre‑built Binaries

Download the latest release for your platform from the [Releases](https://github.com/jackburton-qub/GRACE/releases) page. Extract the folder and run `GRACE.exe` (Windows) or open `GRACE.app` (macOS). BLAST+ is bundled – no separate installation required.

### Running from Source

```bash

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.