Build a Gene Homology Multiple Alignment Quality Ranker — implementation

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

## User
Comparative Genomics Analyst

## Workflow
1. Fetch multi-species homologous gene FASTA packages using taxonomy filters via NCBI Datasets.
2. Perform multiple sequence alignment and calculate gap percentages and conservation scores with Biopython.
3. Detect low-identity outliers exceeding configured alignment distance standard deviations.
4. Serialize alignment summaries into FHIR Molecular DiagnosticReport and Observation bundles.

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

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

## Source
[Biopython](https://raw.githubusercontent.com/biopython/biopython/master/README.rst)
Leverages Biopython's sequence alignment, distance matrix utilities, and FASTA parsing capabilities.

## Tools
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.

## Deliverables
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.

## Acceptance
- 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.

## Starter Examples
```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"
    }
  }
]
```

## Safety
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.