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Project Roadmap

GIAE is an evolving platform. Our goal is to move from sequence-based annotation to a multi-modal structural and functional interpretation engine.

📅 Short-Term (v0.3.0)

🔬 Foldseek / AlphaFold Integration

  • Feature: Use Foldseek to scan the AlphaFold Database (AFDB) for structural homologs.
  • Why: Many phage proteins have zero sequence similarity but conserved 3D folds.
  • Status: Researching Foldseek API integration.

🧪 Bacterial Genome Scaling

  • Feature: Optimized parallel processing for 4–6 Mb genomes.
  • Why: Currently benchmarked on phages; needs better memory management for large bacterial contigs.
  • Status: In development.

📅 Mid-Term (v0.4.0)

🕸️ Evidence Network Visualization

  • Feature: A web-based graph view showing how different evidence types (homology, motifs, domains) conflict or converge for each gene.
  • Status: Prototyping in Javascript.

📊 Comparative Genomics Mode

  • Feature: Diff two interpretations side-by-side to highlight functional divergence between strains.
  • Status: Planned.

📂 Long-Term (v1.0.0)

🧬 Autonomous Annotation Refinement

  • Feature: A self-correcting engine that re-interprets old annotations as new structural data or UniProt reviews become available.
  • Status: Concept phase.