Build a Gene Homology Multiple Alignment Quality Ranker

Align homologous eukaryotic gene transcripts using Biopython and compute conservation density metrics. Package results into FHIR DiagnosticReport payloads for cross-species evolutionary registries.

Comparative Genomics Analyst

Fetch multi-species homologous gene FASTA packages using taxonomy filters via NCBI Datasets.

Perform multiple sequence alignment and calculate gap percentages and conservation scores with Biopython.

Detect low-identity outliers exceeding configured alignment distance standard deviations.

Serialize alignment summaries into FHIR Molecular DiagnosticReport and Observation bundles.

Interactive web visualizer featuring color-coded sequence alignment tracks and gap percentage slider controls.

Curate homologous CDS sequences for mammalian orthologs using NCBI Datasets CLI taxon filters. Starter examples below are synthetic. They are not downloaded records.

Biopython Leverages Biopython's sequence alignment, distance matrix utilities, and FASTA parsing capabilities.

ray-serve, biopython, numpy. ray-serve distributes compute-heavy Biopython alignment jobs and FHIR serialization across parallel worker nodes. Local microservice deployment with multi-core CPU support for alignment processing; optional small language model for report narratives.

Submit runnable source, pinned dependencies, setup commands, a working interface, example outputs, and a recorded end-to-end demo. Include tests and an action log.

Calculate pairwise sequence identity matrices across minimum 5 homologous sequences.

Output FHIR DiagnosticReport containing an Observation with mean conservation score.

Reject sequences containing unparsable non-IUPAC nucleotide characters.

```json [ { "input": { "alignment_id": "ORTHO_001", "sequences": [ { "id": "HUMAN_GENE1", "seq": "ATGCCCAAA" }, { "id": "CHIMP_GENE1", "seq": "ATGCCCAAA" }, { "id": "MOUSE_GENE1", "seq": "ATGCCCAAG" } ] }, "expected_output": { "alignment_id": "ORTHO_001", "mean_identity": 0.963, "outliers": [], "fhir_report": { "resourceType": "DiagnosticReport", "status": "final", "code": { "text": "Homology Alignment Assessment" } } } }, { "input": { "alignment_id": "ORTHO_002", "sequences": [ { "id": "HUMAN_GENE2", "seq": "ATGCCC" }, { "id": "MUTANT_SEQ", "seq": "ATGZZZ" } ] }, "expected_output": { "alignment_id": "ORTHO_002", "mean_identity": null, "outliers": [ "MUTANT_SEQ" ], "error": "Non-IUPAC nucleotide characters identified" } } ] ```

Intended solely for comparative sequence analysis. Contains no personal protected health data or therapeutic determinations. Use mock external writes. Require human review before any real deployment.