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align-sequences

station__dna__align-sequences external (needs EXECUTION_BACKEND_URL) dna non-pv Constructa Configa

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

Taxonomy

Linnaean classification joined from the algovigilance taxonomy index via the parent config's rank.

Rank	Value
domain	`Substrata`
kingdom	`Constructa`
phylum	`Configa`
class	`station-config`
order	`dna`
family	`mcp-tool-config`

Characteristics:

substrate: config
domain: pv
lifecycle: continuous
authority: read
compounding: producer
io: agent-request → tool-response

Input schema

query stringrequired — Query DNA sequence (e.g., 'ATGCGATCGA')
target stringrequired — 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

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

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

How to invoke from a client

From any MCP-aware client, add https://algovigilance.com/api/mcp as an MCP server, then call this tool by name. From a raw HTTP client, send the JSON-RPC body above to /api/mcp.

Agent-friendly formats

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