Build the application

## Build
Align homologous gene transcripts downloaded from public repositories and calculate pairwise distance matrices. Vectorize alignment features into Qdrant to detect anomalous outlier sequences.

## User
Computational Biologist

## Workflow
1. Load homologous FASTA transcripts using Biopython SeqIO.
2. Compute gap frequencies and positional identity matrices across sequence collections.
3. Vectorize alignment summary profiles and index them in a local Qdrant collection.
4. Identify distance outliers and output quality warnings for human curator verification.

## Interface
Streamlit app with interactive distance plots and outlier inspection tables.

## Data
Use Biopython test suite FASTA samples and public viral or eukaryotic homologous transcript sets.
Starter examples below are synthetic. They are not downloaded records.

## Source
[Biopython](https://raw.githubusercontent.com/biopython/biopython/master/README.rst)
Employs Biopython's sequence analysis data structures to parse FASTA alignments and compute residue statistics.

## Tools
qdrant, biopython, streamlit.
Qdrant provides low-latency vector similarity search to cluster alignment score vectors and find outliers.
Small local embedding model or tabular feature projector for alignment metric indexing.

## 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
- Parses multi-sequence FASTA files accurately using Biopython.
- Calculates positional identity and indexes metric vectors into Qdrant.
- Flags sequences with high gap penalties or divergent residue scores.

## Starter Examples
```json
[
  {
    "input": {
      "alignment_id": "ALN-101",
      "sequences": [
        ">seqA\nATGCGATCG",
        ">seqB\nATGCGATCG",
        ">seqC\nATGCGATCA"
      ]
    },
    "expected_output": {
      "alignment_id": "ALN-101",
      "consensus_identity": 0.963,
      "outliers_detected": 0,
      "status": "CONCORDANT"
    }
  },
  {
    "input": {
      "alignment_id": "ALN-102",
      "sequences": [
        ">seqA\nATGCGATCG",
        ">seqB\nNNNNGATCG",
        ">seqC\nATGCGATCG"
      ]
    },
    "expected_output": {
      "alignment_id": "ALN-102",
      "consensus_identity": 0.667,
      "outliers_detected": 1,
      "status": "DISCORDANT_ALERT"
    }
  }
]
```

## Safety
Standard sequence quality profiling tool operating exclusively on open synthetic or public FASTA data.
Use mock external writes. Require human review before any real deployment.