# align-sequences

`station__dna__align-sequences` · external (needs EXECUTION_BACKEND_URL configured) · domain `dna` · pv-relevance `non-pv`

Align two DNA sequences using Smith-Waterman (local) or Needleman-Wunsch (global) algorithm. Returns alignment score, aligned sequences with gaps, and percent identity.

> **Note:** This tool routes through an external execution backend. If `EXECUTION_BACKEND_URL` is unset on the server, calls return JSON-RPC error `-32603 "Tool execution backend not configured"`. Tools with `backend: native` execute in-process and are always callable.

## Agent metadata

- `idempotent`: unknown
- `read_only`: unknown
- `expected_latency_ms`: unknown (not yet contract-tested)
- `cost_tokens_estimate`: unknown

## Input schema

- `query` *string* (required) — Query DNA sequence (e.g., 'ATGCGATCGA')
- `target` *string* (required) — Target DNA sequence to align against
- `method` *string* — Alignment method: 'local' (Smith-Waterman) or 'global' (Needleman-Wunsch). Default: 'local'.
- `match_score` *integer* — Score for matching bases (default: 2)
- `mismatch_score` *integer* — Score for mismatched bases (default: -1)
- `gap_penalty` *integer* — Gap penalty (default: -2)

## Example call

```json
POST /api/mcp
Content-Type: application/json

{
  "jsonrpc": "2.0",
  "id": 1,
  "method": "tools/call",
  "params": {
    "name": "station__dna__align-sequences",
    "arguments": {
      "query": "",
      "target": ""
    }
  }
}
```

## Related

- [/tools](/tools) — all 3062 tools
- [/tools/dna__align-sequences](/tools/dna__align-sequences) — HTML page
- [/tools/dna__align-sequences/json](/tools/dna__align-sequences/json) — JSON form (agent-friendly)
- [/api/mcp](/api/mcp) — endpoint
- [/AGENTS.md](/AGENTS.md) — agent guide