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GIAE — Genome Interpretation & Annotation Engine

Explainability-first genome annotation. Every prediction shows its reasoning.

Most genome annotation tools are overconfident. PROKKA, Bakta, and RAST assign a label, hide the evidence, and give you no way to know how certain the prediction is.

GIAE takes the opposite approach: every gene interpretation includes the full evidence stack, confidence score, uncertainty sources, and a ranked list of competing hypotheses.

🚀 Key Features

  • Multi-layer Evidence: PROSITE motifs, EBI HMMER domains, and UniProt reviews.
  • Confidence Levels: Calibrated scores (HIGH, MODERATE, LOW, SPECULATIVE).
  • Explainable Reporting: Narrative reasoning for every prediction.
  • Novel Gene Discovery: Identifying and ranking "Dark Matter" genes.
  • Parallel Execution: Scalable to large genomes.
  • Flexible Output: Terminal tables, Markdown, and machine-readable JSON.

🛠️ Installation

pip install giae

📖 How it Works

GIAE uses a convergence model. When multiple independent evidence sources (motifs, domains, homology) agree on a function, the confidence is high. When they disagree, GIAE flags the conflict rather than silently resolving it.

Genome (.gb / .fasta)
       │
       ▼
┌──────────────────────────────────────────────┐
│  1. PROSITE Motif Scan         weight: 0.80  │
│  2. EBI HMMER / Pfam Domains   weight: 0.90  │
│  3. UniProt API Lookup         weight: 1.00  │
│  4. Conflict Detection                        │
└──────────────────────────────────────────────┘
       │
       ▼
Interpretation + Confidence Score + Novelty Report