MCP Documentation

Open mcp-config

mitochondria · 38 tools

Overview

Each tool accepts optional parameter api_key: the user's real Mitochondria API key. Never invent, guess, or use placeholder values (undefined, null, test, your-api-key). If the user has not provided a key, the connection's Authorization header or the process MITOCHONDRIA_API_KEY may supply one; still never invent a key. The server forwards the resolved key as Authorization: Bearer so quota applies to that key.

Quotas (standard keys): usage is tracked in token units per UTC calendar day and month. Each successful call may consume a route-specific token cost (configured on the server); if the budget would be exceeded, the API returns HTTP 403 with a quota message (e.g. Payment Required). Admin keys are not quota-limited. Use mitochondria_get_quota_limits to read daily/monthly caps, used amounts, and remainders; that call does not consume tokens.

Successful responses are JSON with status "success" and a "results" field. Malformed JSON often yields 400; validation and business rules often yield 422 with message (and sometimes errors). Each tool description states limits and defaults aligned with the public API documentation.

Persist-then-id protocol for DNA:

1. Persist DNA on first sight (mitochondria_oligos_create or save_results true).

2. Later calls: pass {id} only — do not resend seq or genbank when an id exists.

3. Catalog: mitochondria_catalog_vector_get (GET /catalog/vectors/{name}) → pass {id, name, type: "catalog"} from that response as the backbone handle.

4. Never POST type catalog (users cannot create catalog rows).

5. Prefer primary enzyme names from nested restrictase lists; isoschizomer names remain valid inputs.

6. save_results omits seq/genbank unless full_results is also true; full_results alone is ignored.

Server

  • mitochondriaModel Context Protocol catalog
Quota1 tool
GET/quota/limitsDoes not consume token quota. Returns caps and usage for the current UTC day and month.

tool mitochondria_get_quota_limits

operationId quota_limits_get

Description

Standard keys: daily_limit_tokens, monthly_limit_tokens, daily_used_tokens, monthly_used_tokens,

daily_remaining_tokens, monthly_remaining_tokens, period.utc_day, period.utc_month.

Admin keys: tier admin, unlimited true. Unknown key: 403. Key DB unavailable for non-admin: 503.

Input

{
  "properties": {
    "api_key": {
      "anyOf": [
        {
          "type": "string"
        },
        {
          "type": "null"
        }
      ],
      "default": null,
      "title": "Api Key"
    }
  },
  "title": "mitochondria_get_quota_limitsArguments",
  "type": "object"
}

Output

{
  "properties": {
    "result": {
      "title": "Result",
      "type": "string"
    }
  },
  "required": [
    "result"
  ],
  "title": "mitochondria_get_quota_limitsOutput",
  "type": "object"
}
Sequence4 tools
POST/tools/sequence/reverse_complementDNA or RNA (IUPAC); whitespace stripped, case ignored. Invalid letters: 422.

tool mitochondria_reverse_complement

operationId tools_sequence_reverse_complement

Input

{
  "properties": {
    "api_key": {
      "anyOf": [
        {
          "type": "string"
        },
        {
          "type": "null"
        }
      ],
      "default": null,
      "title": "Api Key"
    },
    "sequence": {
      "title": "Sequence",
      "type": "string"
    }
  },
  "required": [
    "sequence"
  ],
  "title": "mitochondria_reverse_complementArguments",
  "type": "object"
}

Output

{
  "properties": {
    "result": {
      "title": "Result",
      "type": "string"
    }
  },
  "required": [
    "result"
  ],
  "title": "mitochondria_reverse_complementOutput",
  "type": "object"
}
POST/tools/sequence/transcribeDNA to RNA (T→U).

tool mitochondria_sequence_transcribe

operationId tools_sequence_transcribe

Description

Whitespace stripped, case ignored. Invalid symbols: 422.

Input

{
  "properties": {
    "api_key": {
      "anyOf": [
        {
          "type": "string"
        },
        {
          "type": "null"
        }
      ],
      "default": null,
      "title": "Api Key"
    },
    "sequence": {
      "title": "Sequence",
      "type": "string"
    }
  },
  "required": [
    "sequence"
  ],
  "title": "mitochondria_sequence_transcribeArguments",
  "type": "object"
}

Output

{
  "properties": {
    "result": {
      "title": "Result",
      "type": "string"
    }
  },
  "required": [
    "result"
  ],
  "title": "mitochondria_sequence_transcribeOutput",
  "type": "object"
}
POST/tools/sequence/back_transcribeRNA to DNA (U→T).

tool mitochondria_sequence_back_transcribe

operationId tools_sequence_back_transcribe

Description

Whitespace stripped, case ignored. Invalid symbols: 422.

Input

{
  "properties": {
    "api_key": {
      "anyOf": [
        {
          "type": "string"
        },
        {
          "type": "null"
        }
      ],
      "default": null,
      "title": "Api Key"
    },
    "sequence": {
      "title": "Sequence",
      "type": "string"
    }
  },
  "required": [
    "sequence"
  ],
  "title": "mitochondria_sequence_back_transcribeArguments",
  "type": "object"
}

Output

{
  "properties": {
    "result": {
      "title": "Result",
      "type": "string"
    }
  },
  "required": [
    "result"
  ],
  "title": "mitochondria_sequence_back_transcribeOutput",
  "type": "object"
}
POST/tools/sequence/translateDefaults: translation_table=1 (NCBI code), to_stop=false, cds=false. translation_table minimum 1.

tool mitochondria_sequence_translate

operationId tools_sequence_translate

Description

CDS or codon violations: HTTP 422; JSON fields ``message`` and ``errors`` carry the rationale

(cds=true validates start/stop/length/table).

Input

{
  "properties": {
    "api_key": {
      "anyOf": [
        {
          "type": "string"
        },
        {
          "type": "null"
        }
      ],
      "default": null,
      "title": "Api Key"
    },
    "cds": {
      "default": false,
      "title": "Cds",
      "type": "boolean"
    },
    "sequence": {
      "title": "Sequence",
      "type": "string"
    },
    "to_stop": {
      "default": false,
      "title": "To Stop",
      "type": "boolean"
    },
    "translation_table": {
      "anyOf": [
        {
          "type": "integer"
        },
        {
          "type": "null"
        }
      ],
      "default": null,
      "title": "Translation Table"
    }
  },
  "required": [
    "sequence"
  ],
  "title": "mitochondria_sequence_translateArguments",
  "type": "object"
}

Output

{
  "properties": {
    "result": {
      "title": "Result",
      "type": "string"
    }
  },
  "required": [
    "result"
  ],
  "title": "mitochondria_sequence_translateOutput",
  "type": "object"
}
Restriction1 tool
POST/tools/restrictionMulti-enzyme digest map and fragments.

tool mitochondria_tools_restriction

operationId tools_restriction

Description

Default circular=false (linear). Empty restrictase_names: no cuts. circular=true scans as circular topology

(sites may span ends of sequence) and uses wrap-around fragment order first in sequences.

Input

{
  "properties": {
    "api_key": {
      "anyOf": [
        {
          "type": "string"
        },
        {
          "type": "null"
        }
      ],
      "default": null,
      "title": "Api Key"
    },
    "circular": {
      "default": false,
      "title": "Circular",
      "type": "boolean"
    },
    "restrictase_names": {
      "items": {
        "type": "string"
      },
      "title": "Restrictase Names",
      "type": "array"
    },
    "sequence": {
      "title": "Sequence",
      "type": "string"
    }
  },
  "required": [
    "sequence",
    "restrictase_names"
  ],
  "title": "mitochondria_tools_restrictionArguments",
  "type": "object"
}

Output

{
  "properties": {
    "result": {
      "title": "Result",
      "type": "string"
    }
  },
  "required": [
    "result"
  ],
  "title": "mitochondria_tools_restrictionOutput",
  "type": "object"
}
Protein1 tool
POST/tools/protein/reverse_transcribeProtein (one-letter amino acids, * for stop) to coding DNA. host default e.coli

tool mitochondria_protein_reverse_transcribe

operationId tools_protein_reverse_transcribe

Description

(must be a label the service supports). restrictases names enzymes whose sites must

not appear. Invalid symbols: 422. Processing failures return 500.

Input

{
  "properties": {
    "api_key": {
      "anyOf": [
        {
          "type": "string"
        },
        {
          "type": "null"
        }
      ],
      "default": null,
      "title": "Api Key"
    },
    "host": {
      "default": "e.coli",
      "title": "Host",
      "type": "string"
    },
    "restrictases": {
      "items": {
        "type": "string"
      },
      "title": "Restrictases",
      "type": "array"
    },
    "sequence": {
      "title": "Sequence",
      "type": "string"
    }
  },
  "required": [
    "sequence",
    "restrictases"
  ],
  "title": "mitochondria_protein_reverse_transcribeArguments",
  "type": "object"
}

Output

{
  "properties": {
    "result": {
      "title": "Result",
      "type": "string"
    }
  },
  "required": [
    "result"
  ],
  "title": "mitochondria_protein_reverse_transcribeOutput",
  "type": "object"
}
Backbone2 tools
POST/backbone/linearize/selectionExcise segment by positions.

tool mitochondria_backbone_linear_selection

operationId backbone_linear_selection

Description

backbone: object with required id, seq; optional topology (default circular), mcs_start (default 1),

mcs_end (default sequence length).

left_position / right_position: 1-based inclusive segment to remove; right_position may be 0 with

left_position=1 for a seam cut (between last and first base, no bases removed). Alternatively

seam: left=len(seq)+1 and right=len(seq). Adjacent cut (no bases removed): left=right+1.

Optional backbone.genbank: full circular GenBank matching backbone.seq; response may include results.genbank

(linear record with remapped features).

Input

{
  "properties": {
    "api_key": {
      "anyOf": [
        {
          "type": "string"
        },
        {
          "type": "null"
        }
      ],
      "default": null,
      "title": "Api Key"
    },
    "backbone": {
      "title": "Backbone",
      "type": "object"
    },
    "left_position": {
      "title": "Left Position",
      "type": "integer"
    },
    "right_position": {
      "title": "Right Position",
      "type": "integer"
    }
  },
  "required": [
    "backbone",
    "left_position",
    "right_position"
  ],
  "title": "mitochondria_backbone_linear_selectionArguments",
  "type": "object"
}

Output

{
  "properties": {
    "result": {
      "title": "Result",
      "type": "string"
    }
  },
  "required": [
    "result"
  ],
  "title": "mitochondria_backbone_linear_selectionOutput",
  "type": "object"
}
POST/backbone/linearize/restrictionbackbone: id and seq required; optional topology, mcs_start, mcs_end as documented in the public API.

tool mitochondria_backbone_linear_restriction

operationId backbone_linear_restriction

Description

For a single enzyme, pass end_restrictase as '' (empty string). Enzyme names from server catalog.

With two enzymes, returns the linearized vector backbone (long fragment); not the MCS insert-sized dropout.

Input

{
  "properties": {
    "api_key": {
      "anyOf": [
        {
          "type": "string"
        },
        {
          "type": "null"
        }
      ],
      "default": null,
      "title": "Api Key"
    },
    "backbone": {
      "title": "Backbone",
      "type": "object"
    },
    "end_restrictase": {
      "title": "End Restrictase",
      "type": "string"
    },
    "start_restrictase": {
      "title": "Start Restrictase",
      "type": "string"
    }
  },
  "required": [
    "backbone",
    "start_restrictase",
    "end_restrictase"
  ],
  "title": "mitochondria_backbone_linear_restrictionArguments",
  "type": "object"
}

Output

{
  "properties": {
    "result": {
      "title": "Result",
      "type": "string"
    }
  },
  "required": [
    "result"
  ],
  "title": "mitochondria_backbone_linear_restrictionOutput",
  "type": "object"
}
Primers1 tool
POST/primers/simpleSimple PCR primers for a linear insert.

tool mitochondria_primers_simple

operationId primers_simple

Description

options optional: min_tm default 60 (allowed 50–80 °C); min_length default 18 (allowed 15–35 bp;

alias min_primer_length).

RNA-like insert (U) is coerced to T with a warning. No primers found: often 500.

Reported melting_temperature / annealing_temperature follow the public API definitions

(nearest-neighbour + mixed-ion oligomer assumptions).

overwrite applies when saving an oligo input (existing id without overwrite: 409).

Input

{
  "properties": {
    "api_key": {
      "anyOf": [
        {
          "type": "string"
        },
        {
          "type": "null"
        }
      ],
      "default": null,
      "title": "Api Key"
    },
    "insert": {
      "title": "Insert",
      "type": "object"
    },
    "options": {
      "anyOf": [
        {
          "type": "object"
        },
        {
          "type": "null"
        }
      ],
      "default": null,
      "title": "Options"
    },
    "overwrite": {
      "default": false,
      "title": "Overwrite",
      "type": "boolean"
    }
  },
  "required": [
    "insert"
  ],
  "title": "mitochondria_primers_simpleArguments",
  "type": "object"
}

Output

{
  "properties": {
    "result": {
      "title": "Result",
      "type": "string"
    }
  },
  "required": [
    "result"
  ],
  "title": "mitochondria_primers_simpleOutput",
  "type": "object"
}
Restriction cloning5 tools
POST/cloning/restriction/primersinsert: {id, seq}. restrictases: {start, end} enzyme names; optional start_seq, end_seq.

tool mitochondria_restriction_cloning_primers

operationId restriction_cloning_primers

Description

options optional: start_overhang_size, end_overhang_size in 1–5 bp when set.

overwrite applies when saving an oligo input (existing id without overwrite: 409).

Input

{
  "properties": {
    "api_key": {
      "anyOf": [
        {
          "type": "string"
        },
        {
          "type": "null"
        }
      ],
      "default": null,
      "title": "Api Key"
    },
    "forward_primer": {
      "title": "Forward Primer",
      "type": "string"
    },
    "insert": {
      "title": "Insert",
      "type": "object"
    },
    "options": {
      "anyOf": [
        {
          "type": "object"
        },
        {
          "type": "null"
        }
      ],
      "default": null,
      "title": "Options"
    },
    "overwrite": {
      "default": false,
      "title": "Overwrite",
      "type": "boolean"
    },
    "restrictases": {
      "title": "Restrictases",
      "type": "object"
    },
    "reverse_primer": {
      "title": "Reverse Primer",
      "type": "string"
    }
  },
  "required": [
    "insert",
    "forward_primer",
    "reverse_primer",
    "restrictases"
  ],
  "title": "mitochondria_restriction_cloning_primersArguments",
  "type": "object"
}

Output

{
  "properties": {
    "result": {
      "title": "Result",
      "type": "string"
    }
  },
  "required": [
    "result"
  ],
  "title": "mitochondria_restriction_cloning_primersOutput",
  "type": "object"
}
POST/cloning/restriction/primers_combinedAuto simple-primer step then adds sites like /cloning/restriction/primers.

tool mitochondria_restriction_cloning_primers_combined

operationId restriction_cloning_primers_combined

Description

options optional: overhang sizes 1–5; min_tm if set must be strictly between 30 and 100 °C.

If min_tm omitted, inner step uses default 60 °C like /primers/simple. min_length 15–35 bp (default 18)

for the inner simple-primer step; min_primer_length alias supported.

overwrite applies when saving an oligo input (existing id without overwrite: 409).

Input

{
  "properties": {
    "api_key": {
      "anyOf": [
        {
          "type": "string"
        },
        {
          "type": "null"
        }
      ],
      "default": null,
      "title": "Api Key"
    },
    "insert": {
      "title": "Insert",
      "type": "object"
    },
    "options": {
      "anyOf": [
        {
          "type": "object"
        },
        {
          "type": "null"
        }
      ],
      "default": null,
      "title": "Options"
    },
    "overwrite": {
      "default": false,
      "title": "Overwrite",
      "type": "boolean"
    },
    "restrictases": {
      "title": "Restrictases",
      "type": "object"
    }
  },
  "required": [
    "insert",
    "restrictases"
  ],
  "title": "mitochondria_restriction_cloning_primers_combinedArguments",
  "type": "object"
}

Output

{
  "properties": {
    "result": {
      "title": "Result",
      "type": "string"
    }
  },
  "required": [
    "result"
  ],
  "title": "mitochondria_restriction_cloning_primers_combinedOutput",
  "type": "object"
}
POST/cloning/restriction/restrictioninserts: array of {id, seq}, max 10 items; empty array = backbone-only enzyme context.

tool mitochondria_restriction_cloning_restrictases

operationId restriction_cloning_restrictases

Input

{
  "properties": {
    "api_key": {
      "anyOf": [
        {
          "type": "string"
        },
        {
          "type": "null"
        }
      ],
      "default": null,
      "title": "Api Key"
    },
    "backbone": {
      "title": "Backbone",
      "type": "object"
    },
    "inserts": {
      "items": {
        "type": "object"
      },
      "title": "Inserts",
      "type": "array"
    }
  },
  "required": [
    "backbone",
    "inserts"
  ],
  "title": "mitochondria_restriction_cloning_restrictasesArguments",
  "type": "object"
}

Output

{
  "properties": {
    "result": {
      "title": "Result",
      "type": "string"
    }
  },
  "required": [
    "result"
  ],
  "title": "mitochondria_restriction_cloning_restrictasesOutput",
  "type": "object"
}
GET/cloning/restriction/restriction/supported_restrictasesoperationId: restriction_cloning_supported_restrictases_get.

tool mitochondria_restriction_cloning_supported_restrictases

Description

Alphabetically sorted sticky Type IIP enzyme names used for restriction-cloning MCS logic.

Input

{
  "properties": {
    "api_key": {
      "anyOf": [
        {
          "type": "string"
        },
        {
          "type": "null"
        }
      ],
      "default": null,
      "title": "Api Key"
    }
  },
  "title": "mitochondria_restriction_cloning_supported_restrictasesArguments",
  "type": "object"
}

Output

{
  "properties": {
    "result": {
      "title": "Result",
      "type": "string"
    }
  },
  "required": [
    "result"
  ],
  "title": "mitochondria_restriction_cloning_supported_restrictasesOutput",
  "type": "object"
}
POST/cloning/restriction/resultRequired request fields: backbone (with genbank), construct_name, insert,

tool mitochondria_restriction_cloning_result

operationId restriction_cloning_result

Description

insert_name, insert_type, insertion_position_1, forward_primer_full_seq,

reverse_primer_full_seq, forward_primer_restrictase_position,

reverse_primer_restrictase_position; optional insertion_position_2,

forward_primer_restrictase, reverse_primer_restrictase.

Integer positions are >= 1 where specified. backbone.genbank is full GenBank text including ORIGIN and //.

Success: results is GenBank text. primer_bind features use /label with the restrictase name when

that name is recognized in the supported enzyme catalog; otherwise labels are forward_primer /

reverse_primer. /note still describes the restriction-site remnant.

Input

{
  "properties": {
    "api_key": {
      "anyOf": [
        {
          "type": "string"
        },
        {
          "type": "null"
        }
      ],
      "default": null,
      "title": "Api Key"
    },
    "body": {
      "title": "Body",
      "type": "object"
    }
  },
  "required": [
    "body"
  ],
  "title": "mitochondria_restriction_cloning_resultArguments",
  "type": "object"
}

Output

{
  "properties": {
    "result": {
      "title": "Result",
      "type": "string"
    }
  },
  "required": [
    "result"
  ],
  "title": "mitochondria_restriction_cloning_resultOutput",
  "type": "object"
}
PCR cloning3 tools
POST/cloning/pcr/constructsTwo concatamer previews.

tool mitochondria_pcr_cloning_constructs

operationId pcr_cloning_constructs

Description

backbone and insert are oligo objects with seq; else 422.

Input

{
  "properties": {
    "api_key": {
      "anyOf": [
        {
          "type": "string"
        },
        {
          "type": "null"
        }
      ],
      "default": null,
      "title": "Api Key"
    },
    "backbone": {
      "title": "Backbone",
      "type": "object"
    },
    "insert": {
      "title": "Insert",
      "type": "object"
    }
  },
  "required": [
    "backbone",
    "insert"
  ],
  "title": "mitochondria_pcr_cloning_constructsArguments",
  "type": "object"
}

Output

{
  "properties": {
    "result": {
      "title": "Result",
      "type": "string"
    }
  },
  "required": [
    "result"
  ],
  "title": "mitochondria_pcr_cloning_constructsOutput",
  "type": "object"
}
POST/cloning/pcr/restrictionBlunt single-cutters in MCS.

tool mitochondria_pcr_cloning_restriction

operationId pcr_cloning_restriction

Description

Circular backbone only; linear backbone returns empty results []. Cuts once, blunt, site in mcs_start…mcs_end.

Input

{
  "properties": {
    "api_key": {
      "anyOf": [
        {
          "type": "string"
        },
        {
          "type": "null"
        }
      ],
      "default": null,
      "title": "Api Key"
    },
    "backbone": {
      "title": "Backbone",
      "type": "object"
    }
  },
  "required": [
    "backbone"
  ],
  "title": "mitochondria_pcr_cloning_restrictionArguments",
  "type": "object"
}

Output

{
  "properties": {
    "result": {
      "title": "Result",
      "type": "string"
    }
  },
  "required": [
    "result"
  ],
  "title": "mitochondria_pcr_cloning_restrictionOutput",
  "type": "object"
}
POST/cloning/pcr/resultRequired request fields: backbone (with genbank), construct_name, insert, insert_name,

tool mitochondria_pcr_cloning_result

operationId pcr_cloning_result

Description

insert_type, insertion_position_1; optional insertion_position_2, forward_primer,

reverse_primer, restrictase_names, use_reverse_complement (default false).

Positions minimum 1. Success: results is GenBank text string.

Input

{
  "properties": {
    "api_key": {
      "anyOf": [
        {
          "type": "string"
        },
        {
          "type": "null"
        }
      ],
      "default": null,
      "title": "Api Key"
    },
    "body": {
      "title": "Body",
      "type": "object"
    }
  },
  "required": [
    "body"
  ],
  "title": "mitochondria_pcr_cloning_resultArguments",
  "type": "object"
}

Output

{
  "properties": {
    "result": {
      "title": "Result",
      "type": "string"
    }
  },
  "required": [
    "result"
  ],
  "title": "mitochondria_pcr_cloning_resultOutput",
  "type": "object"
}
Gibson cloning4 tools
POST/cloning/gibson/primersOligo contract: insert/backbone use {id}, {seq}, or catalog {id, name, type: "catalog"}.

tool mitochondria_gibson_cloning_primers

operationId gibson_cloning_primers

Description

Prefer ids after persist; do not resend seq/genbank when an id exists.

Provide both start_overlap_seq and end_overlap_seq, or omit both and supply backbone plus

restrictase (single MCS cut of a circular backbone). One overlap without the other, or

neither a complete overlap pair nor backbone+restrictase, is rejected.

Required options: primer_tm, overlap_tm (°C); overlap_size (bp, >= 1). add_kozak designs

forward annealing against GCCACC 5' of an ATG-starting insert.

Input

{
  "properties": {
    "add_kozak": {
      "default": false,
      "title": "Add Kozak",
      "type": "boolean"
    },
    "api_key": {
      "anyOf": [
        {
          "type": "string"
        },
        {
          "type": "null"
        }
      ],
      "default": null,
      "title": "Api Key"
    },
    "backbone": {
      "anyOf": [
        {
          "type": "object"
        },
        {
          "type": "null"
        }
      ],
      "default": null,
      "title": "Backbone"
    },
    "end_overlap_seq": {
      "anyOf": [
        {
          "type": "string"
        },
        {
          "type": "null"
        }
      ],
      "default": null,
      "title": "End Overlap Seq"
    },
    "insert": {
      "title": "Insert",
      "type": "object"
    },
    "overlap_size": {
      "title": "Overlap Size",
      "type": "integer"
    },
    "overlap_tm": {
      "title": "Overlap Tm",
      "type": "integer"
    },
    "primer_tm": {
      "title": "Primer Tm",
      "type": "integer"
    },
    "restrictase": {
      "anyOf": [
        {
          "type": "string"
        },
        {
          "type": "null"
        }
      ],
      "default": null,
      "title": "Restrictase"
    },
    "start_overlap_seq": {
      "anyOf": [
        {
          "type": "string"
        },
        {
          "type": "null"
        }
      ],
      "default": null,
      "title": "Start Overlap Seq"
    }
  },
  "required": [
    "insert",
    "primer_tm",
    "overlap_size",
    "overlap_tm"
  ],
  "title": "mitochondria_gibson_cloning_primersArguments",
  "type": "object"
}

Output

{
  "properties": {
    "result": {
      "title": "Result",
      "type": "string"
    }
  },
  "required": [
    "result"
  ],
  "title": "mitochondria_gibson_cloning_primersOutput",
  "type": "object"
}
POST/cloning/gibson/resultOligo contract: backbone/insert use {id}, inline seq/genbank, or catalog

tool mitochondria_gibson_cloning_result

operationId gibson_cloning_result

Description

{id, name, type: "catalog"} (no seq paste after catalog get). Prefer ids.

Assembles a circular plasmid; restrictase must cut once in the MCS. Primers are the full

sequences from /cloning/gibson/primers. Backbone must resolve to GenBank (catalog/stored/

inline). construct_name required. add_kozak must match primer design.

save_results: compact construct handle (no genbank) unless full_results also true;

full_results alone is ignored.

Input

{
  "properties": {
    "add_kozak": {
      "default": false,
      "title": "Add Kozak",
      "type": "boolean"
    },
    "api_key": {
      "anyOf": [
        {
          "type": "string"
        },
        {
          "type": "null"
        }
      ],
      "default": null,
      "title": "Api Key"
    },
    "backbone": {
      "title": "Backbone",
      "type": "object"
    },
    "construct_name": {
      "title": "Construct Name",
      "type": "string"
    },
    "forward_primer_full_seq": {
      "title": "Forward Primer Full Seq",
      "type": "string"
    },
    "full_results": {
      "default": false,
      "title": "Full Results",
      "type": "boolean"
    },
    "insert": {
      "title": "Insert",
      "type": "object"
    },
    "insert_name": {
      "anyOf": [
        {
          "type": "string"
        },
        {
          "type": "null"
        }
      ],
      "default": null,
      "title": "Insert Name"
    },
    "insert_type": {
      "default": "CDS",
      "title": "Insert Type",
      "type": "string"
    },
    "overwrite": {
      "default": false,
      "title": "Overwrite",
      "type": "boolean"
    },
    "restrictase": {
      "title": "Restrictase",
      "type": "string"
    },
    "reverse_primer_full_seq": {
      "title": "Reverse Primer Full Seq",
      "type": "string"
    },
    "save_results": {
      "default": false,
      "title": "Save Results",
      "type": "boolean"
    }
  },
  "required": [
    "backbone",
    "insert",
    "restrictase",
    "construct_name",
    "forward_primer_full_seq",
    "reverse_primer_full_seq"
  ],
  "title": "mitochondria_gibson_cloning_resultArguments",
  "type": "object"
}

Output

{
  "properties": {
    "result": {
      "title": "Result",
      "type": "string"
    }
  },
  "required": [
    "result"
  ],
  "title": "mitochondria_gibson_cloning_resultOutput",
  "type": "object"
}
POST/cloning/gibson/restrictionType IIP enzymes cutting once in MCS; circular backbone only (linear returns []).

tool mitochondria_gibson_cloning_restrictases

operationId gibson_cloning_restrictases

Input

{
  "properties": {
    "api_key": {
      "anyOf": [
        {
          "type": "string"
        },
        {
          "type": "null"
        }
      ],
      "default": null,
      "title": "Api Key"
    },
    "backbone": {
      "title": "Backbone",
      "type": "object"
    }
  },
  "required": [
    "backbone"
  ],
  "title": "mitochondria_gibson_cloning_restrictasesArguments",
  "type": "object"
}

Output

{
  "properties": {
    "result": {
      "title": "Result",
      "type": "string"
    }
  },
  "required": [
    "result"
  ],
  "title": "mitochondria_gibson_cloning_restrictasesOutput",
  "type": "object"
}
GET/cloning/gibson/restriction/supported_restrictasesAlphabetically sorted Type IIP enzyme names (sticky or blunt) used for Gibson vector-linearization MCS logic.

tool mitochondria_gibson_cloning_supported_restrictases

operationId gibson_cloning_supported_restrictases_get

Input

{
  "properties": {
    "api_key": {
      "anyOf": [
        {
          "type": "string"
        },
        {
          "type": "null"
        }
      ],
      "default": null,
      "title": "Api Key"
    }
  },
  "title": "mitochondria_gibson_cloning_supported_restrictasesArguments",
  "type": "object"
}

Output

{
  "properties": {
    "result": {
      "title": "Result",
      "type": "string"
    }
  },
  "required": [
    "result"
  ],
  "title": "mitochondria_gibson_cloning_supported_restrictasesOutput",
  "type": "object"
}
Golden Gate5 tools
POST/cloning/golden_gate/restrictionType IIS enzymes for Golden Gate assembly; inserts max 10. preferred_restrictases optional reordering hint.

tool mitochondria_golden_gate_cloning_restrictases

operationId golden_gate_cloning_restrictases

Input

{
  "properties": {
    "api_key": {
      "anyOf": [
        {
          "type": "string"
        },
        {
          "type": "null"
        }
      ],
      "default": null,
      "title": "Api Key"
    },
    "backbone": {
      "title": "Backbone",
      "type": "object"
    },
    "inserts": {
      "items": {
        "type": "object"
      },
      "title": "Inserts",
      "type": "array"
    },
    "preferred_restrictases": {
      "anyOf": [
        {
          "items": {
            "type": "string"
          },
          "type": "array"
        },
        {
          "type": "null"
        }
      ],
      "default": null,
      "title": "Preferred Restrictases"
    }
  },
  "required": [
    "backbone",
    "inserts"
  ],
  "title": "mitochondria_golden_gate_cloning_restrictasesArguments",
  "type": "object"
}

Output

{
  "properties": {
    "result": {
      "title": "Result",
      "type": "string"
    }
  },
  "required": [
    "result"
  ],
  "title": "mitochondria_golden_gate_cloning_restrictasesOutput",
  "type": "object"
}
POST/cloning/golden_gate/cassetteDetect whether the backbone MCS contains a Type IIS cassette (two same-enzyme sites).

tool mitochondria_golden_gate_cassette_detect

operationId golden_gate_cassette_detect

Input

{
  "properties": {
    "api_key": {
      "anyOf": [
        {
          "type": "string"
        },
        {
          "type": "null"
        }
      ],
      "default": null,
      "title": "Api Key"
    },
    "backbone": {
      "title": "Backbone",
      "type": "object"
    }
  },
  "required": [
    "backbone"
  ],
  "title": "mitochondria_golden_gate_cassette_detectArguments",
  "type": "object"
}

Output

{
  "properties": {
    "result": {
      "title": "Result",
      "type": "string"
    }
  },
  "required": [
    "result"
  ],
  "title": "mitochondria_golden_gate_cassette_detectOutput",
  "type": "object"
}
GET/cloning/golden_gate/restriction/supported_restrictasesoperationId: golden_gate_cloning_supported_restrictases_get.

tool mitochondria_golden_gate_cloning_supported_restrictases

Description

Alphabetically sorted Type IIS enzyme names used for Golden Gate planning.

Input

{
  "properties": {
    "api_key": {
      "anyOf": [
        {
          "type": "string"
        },
        {
          "type": "null"
        }
      ],
      "default": null,
      "title": "Api Key"
    }
  },
  "title": "mitochondria_golden_gate_cloning_supported_restrictasesArguments",
  "type": "object"
}

Output

{
  "properties": {
    "result": {
      "title": "Result",
      "type": "string"
    }
  },
  "required": [
    "result"
  ],
  "title": "mitochondria_golden_gate_cloning_supported_restrictasesOutput",
  "type": "object"
}
POST/cloning/golden_gate/primersDesigns Type IIS insert primers for Golden Gate assembly in the given insert order.

tool mitochondria_golden_gate_cloning_primers

operationId golden_gate_cloning_primers

Description

Backbone must have an inward cassette for restrictase (catalog primary name or isoschizomer).

inserts max 10. Cassette fusion sites are never client-overridable.

internal_overhangs optional: one pin or null per junction between inserts (length = len(inserts)-1);

omit for a single insert. Pins must be DNA A/C/G/T, native sticky-end length, non-palindromic,

unique, and not equal to cassette ends.

options optional: min_tm if set must be strictly between 30 and 100 °C (omit for default 60 °C

like simple PCR primers); min_length 15–35 bp (default 18).

Inserts that still contain the enzyme recognition site are rejected (codon-optimize first).

overwrite applies when saving oligo inputs (existing id without overwrite: 409).

Input

{
  "properties": {
    "api_key": {
      "anyOf": [
        {
          "type": "string"
        },
        {
          "type": "null"
        }
      ],
      "default": null,
      "title": "Api Key"
    },
    "backbone": {
      "title": "Backbone",
      "type": "object"
    },
    "inserts": {
      "items": {
        "type": "object"
      },
      "title": "Inserts",
      "type": "array"
    },
    "internal_overhangs": {
      "anyOf": [
        {
          "items": {
            "anyOf": [
              {
                "type": "string"
              },
              {
                "type": "null"
              }
            ]
          },
          "type": "array"
        },
        {
          "type": "null"
        }
      ],
      "default": null,
      "title": "Internal Overhangs"
    },
    "options": {
      "anyOf": [
        {
          "type": "object"
        },
        {
          "type": "null"
        }
      ],
      "default": null,
      "title": "Options"
    },
    "overwrite": {
      "default": false,
      "title": "Overwrite",
      "type": "boolean"
    },
    "restrictase": {
      "title": "Restrictase",
      "type": "string"
    }
  },
  "required": [
    "backbone",
    "inserts",
    "restrictase"
  ],
  "title": "mitochondria_golden_gate_cloning_primersArguments",
  "type": "object"
}

Output

{
  "properties": {
    "result": {
      "title": "Result",
      "type": "string"
    }
  },
  "required": [
    "result"
  ],
  "title": "mitochondria_golden_gate_cloning_primersOutput",
  "type": "object"
}
POST/cloning/golden_gate/resultAssembles a circular plasmid from a cassette backbone and ordered Type IIS-flanked PCR

tool mitochondria_golden_gate_cloning_result

operationId golden_gate_cloning_result

Description

products. Backbone must be circular with an inward cassette for restrictase (catalog

primary name or isoschizomer). PCR product order is assembly order; each product must

digest to sticky ends that match cassette left, successive insert fusions, then cassette

right. construct_name is required and must be non-empty.

Put optional destination GenBank on backbone.genbank.

insert_features optional: annotation overrides by product id (name, type; type defaults

to CDS). Success: results is circular GenBank text.

Input

{
  "properties": {
    "api_key": {
      "anyOf": [
        {
          "type": "string"
        },
        {
          "type": "null"
        }
      ],
      "default": null,
      "title": "Api Key"
    },
    "backbone": {
      "title": "Backbone",
      "type": "object"
    },
    "construct_name": {
      "title": "Construct Name",
      "type": "string"
    },
    "insert_features": {
      "anyOf": [
        {
          "items": {
            "type": "object"
          },
          "type": "array"
        },
        {
          "type": "null"
        }
      ],
      "default": null,
      "title": "Insert Features"
    },
    "pcr_products": {
      "items": {
        "type": "object"
      },
      "title": "Pcr Products",
      "type": "array"
    },
    "restrictase": {
      "title": "Restrictase",
      "type": "string"
    }
  },
  "required": [
    "backbone",
    "pcr_products",
    "restrictase",
    "construct_name"
  ],
  "title": "mitochondria_golden_gate_cloning_resultArguments",
  "type": "object"
}

Output

{
  "properties": {
    "result": {
      "title": "Result",
      "type": "string"
    }
  },
  "required": [
    "result"
  ],
  "title": "mitochondria_golden_gate_cloning_resultOutput",
  "type": "object"
}
Cloning design1 tool
POST/cloning/design/experimentInteractive cloning design: answer strategy questions, then optionally supply backbone/inserts

tool mitochondria_design_cloning_experiment

operationId design_cloning_experiment

Description

for compatibility checks and a workflow plan. answers keys: insert_orientation (random|defined),

inserts_per_backbone (int), is_modular (bool). execute default false; when true runs workflow steps

inline including primers and GenBank when execution_context is provided. inserts max 10.

Input

{
  "properties": {
    "answers": {
      "anyOf": [
        {
          "type": "object"
        },
        {
          "type": "null"
        }
      ],
      "default": null,
      "title": "Answers"
    },
    "api_key": {
      "anyOf": [
        {
          "type": "string"
        },
        {
          "type": "null"
        }
      ],
      "default": null,
      "title": "Api Key"
    },
    "backbone": {
      "anyOf": [
        {
          "type": "object"
        },
        {
          "type": "null"
        }
      ],
      "default": null,
      "title": "Backbone"
    },
    "execute": {
      "default": false,
      "title": "Execute",
      "type": "boolean"
    },
    "execution_context": {
      "anyOf": [
        {
          "type": "object"
        },
        {
          "type": "null"
        }
      ],
      "default": null,
      "title": "Execution Context"
    },
    "inserts": {
      "anyOf": [
        {
          "items": {
            "type": "object"
          },
          "type": "array"
        },
        {
          "type": "null"
        }
      ],
      "default": null,
      "title": "Inserts"
    },
    "preferred_restrictases": {
      "anyOf": [
        {
          "items": {
            "type": "string"
          },
          "type": "array"
        },
        {
          "type": "null"
        }
      ],
      "default": null,
      "title": "Preferred Restrictases"
    }
  },
  "title": "mitochondria_design_cloning_experimentArguments",
  "type": "object"
}

Output

{
  "properties": {
    "result": {
      "title": "Result",
      "type": "string"
    }
  },
  "required": [
    "result"
  ],
  "title": "mitochondria_design_cloning_experimentOutput",
  "type": "object"
}
Codon optimization1 tool
POST/codon/optimizationinsert is an oligo object. A stored {id} loads this key's row; {seq} is inline; {id, seq} saves.

tool mitochondria_codon_optimization

operationId codon_optimization

Description

host default e.coli (must be a label the service supports). restriction_sites_only default false

(true = recode only codons overlapping listed enzyme sites).

overwrite applies when saving the input oligo (existing id without overwrite: 409).

save_results true stores the optimized DNA as an insert and returns a compact handle plus

summary unless full_results is also true (then optimized_seq is included too). New rows that

would exceed the stored-oligo cap (default 100) are 403 (Forbidden, not token Payment Required).

Input

{
  "properties": {
    "api_key": {
      "anyOf": [
        {
          "type": "string"
        },
        {
          "type": "null"
        }
      ],
      "default": null,
      "title": "Api Key"
    },
    "full_results": {
      "default": false,
      "title": "Full Results",
      "type": "boolean"
    },
    "host": {
      "default": "e.coli",
      "title": "Host",
      "type": "string"
    },
    "insert": {
      "title": "Insert",
      "type": "object"
    },
    "overwrite": {
      "default": false,
      "title": "Overwrite",
      "type": "boolean"
    },
    "restrictases": {
      "items": {
        "type": "string"
      },
      "title": "Restrictases",
      "type": "array"
    },
    "restriction_sites_only": {
      "default": false,
      "title": "Restriction Sites Only",
      "type": "boolean"
    },
    "save_results": {
      "default": false,
      "title": "Save Results",
      "type": "boolean"
    }
  },
  "required": [
    "restrictases",
    "insert"
  ],
  "title": "mitochondria_codon_optimizationArguments",
  "type": "object"
}

Output

{
  "properties": {
    "result": {
      "title": "Result",
      "type": "string"
    }
  },
  "required": [
    "result"
  ],
  "title": "mitochondria_codon_optimizationOutput",
  "type": "object"
}
Mutations2 tools
POST/mutations/designResolves a mutation notation against a complete CDS and returns the codon edit that

tool mitochondria_mutation_design

operationId mutation_design

Description

realizes it, without changing the sequence. insert must start with ATG, have a length

divisible by three, and end with an in-frame stop codon; otherwise 422.

mutation_notation accepts protein shorthand (G12D or p.G12D), three-letter protein form

(p.Gly12Asp), or a coding substitution (c.35G>A). The wild-type residue or base must match

the sequence, and the position must be inside it; mismatches and unrecognized notations

are 422. Results: protein_change, coding_change, wildtype_codon, mutant_codon, cds_position.

insert is an oligo object. A stored {id} loads this key's row; {seq} is inline; {id, seq} saves.

overwrite applies when saving the input oligo (existing id without overwrite: 409).

Input

{
  "properties": {
    "api_key": {
      "anyOf": [
        {
          "type": "string"
        },
        {
          "type": "null"
        }
      ],
      "default": null,
      "title": "Api Key"
    },
    "insert": {
      "title": "Insert",
      "type": "object"
    },
    "mutation_notation": {
      "title": "Mutation Notation",
      "type": "string"
    },
    "overwrite": {
      "default": false,
      "title": "Overwrite",
      "type": "boolean"
    }
  },
  "required": [
    "insert",
    "mutation_notation"
  ],
  "title": "mitochondria_mutation_designArguments",
  "type": "object"
}

Output

{
  "properties": {
    "result": {
      "title": "Result",
      "type": "string"
    }
  },
  "required": [
    "result"
  ],
  "title": "mitochondria_mutation_designOutput",
  "type": "object"
}
POST/mutations/applyOligo contract: insert is {id}, {seq}, or {id, seq} (save). Prefer {id} after persist.

tool mitochondria_mutation_apply

operationId mutation_apply

Description

Applies ordered substitutions to a complete CDS. Each mutations entry has coding_change

and/or mutation_notation; empty list is 422. Double mutants are two entries.

Without save_results: seq, protein_translation, warnings, applied. With save_results:

compact insert handle plus summary (no seq) unless full_results also true;

full_results alone is ignored.

Input

{
  "properties": {
    "api_key": {
      "anyOf": [
        {
          "type": "string"
        },
        {
          "type": "null"
        }
      ],
      "default": null,
      "title": "Api Key"
    },
    "full_results": {
      "default": false,
      "title": "Full Results",
      "type": "boolean"
    },
    "insert": {
      "title": "Insert",
      "type": "object"
    },
    "mutations": {
      "items": {
        "type": "object"
      },
      "title": "Mutations",
      "type": "array"
    },
    "overwrite": {
      "default": false,
      "title": "Overwrite",
      "type": "boolean"
    },
    "save_results": {
      "default": false,
      "title": "Save Results",
      "type": "boolean"
    }
  },
  "required": [
    "insert",
    "mutations"
  ],
  "title": "mitochondria_mutation_applyArguments",
  "type": "object"
}

Output

{
  "properties": {
    "result": {
      "title": "Result",
      "type": "string"
    }
  },
  "required": [
    "result"
  ],
  "title": "mitochondria_mutation_applyOutput",
  "type": "object"
}
Constructs1 tool
POST/constructs/validateChecks an assembled construct against what the experiment intended, without changing it.

tool mitochondria_construct_validate

operationId construct_validate

Description

construct is an oligo object that must resolve to a GenBank record: {genbank} is inline,

a stored {id} loads this key's construct, {id, genbank} saves then validates.

The insert coding sequence is the annotated CDS feature — the one matching expected_insert

when given, otherwise the first CDS that a promoter reads toward (the first CDS on the

record when no promoter reads toward any of them).

Results: validation_passed plus checks with reading_frame_preserved (CDS length divisible

by three and starting at ATG), premature_stop_codons (TRUE means an in-frame stop appears

before the last codon, which is a failure), orientation_correct (CDS on the same strand as

the promoter that drives it), promoter_compatible (a promoter feature, or a feature labelled

CMV, lies upstream of the CDS in its own reading direction), and mutation_present.

mutation_present is true when the CDS contains expected_insert DNA and its translation

carries expected_protein_change (G12D, p.G12D, or p.Gly12Asp); with no expectation it is

true. validation_passed requires every check true and premature_stop_codons false.

Failed checks are 200 with false flags; a missing or unreadable GenBank record, a record

with no CDS, and unrecognized mutation notation are 422.

overwrite applies when saving an oligo input (existing id without overwrite: 409).

Input

{
  "properties": {
    "api_key": {
      "anyOf": [
        {
          "type": "string"
        },
        {
          "type": "null"
        }
      ],
      "default": null,
      "title": "Api Key"
    },
    "construct": {
      "title": "Construct",
      "type": "object"
    },
    "expected_insert": {
      "anyOf": [
        {
          "type": "object"
        },
        {
          "type": "null"
        }
      ],
      "default": null,
      "title": "Expected Insert"
    },
    "expected_protein_change": {
      "anyOf": [
        {
          "type": "string"
        },
        {
          "type": "null"
        }
      ],
      "default": null,
      "title": "Expected Protein Change"
    },
    "overwrite": {
      "default": false,
      "title": "Overwrite",
      "type": "boolean"
    }
  },
  "required": [
    "construct"
  ],
  "title": "mitochondria_construct_validateArguments",
  "type": "object"
}

Output

{
  "properties": {
    "result": {
      "title": "Result",
      "type": "string"
    }
  },
  "required": [
    "result"
  ],
  "title": "mitochondria_construct_validateOutput",
  "type": "object"
}
Oligos4 tools
POST/oligosPersist DNA under this key for later {id}-only reuse. type required: insert,

tool mitochondria_oligos_create

operationId oligos_create

Description

backbone, or construct (never catalog — 422). Provide seq and/or genbank (must

match if both). Omit id for a server UUID. overwrite default false (409 on

conflicting rewrite). Cap exceeded: 403. Success 201 with full stored oligo.

Input

{
  "properties": {
    "api_key": {
      "anyOf": [
        {
          "type": "string"
        },
        {
          "type": "null"
        }
      ],
      "default": null,
      "title": "Api Key"
    },
    "genbank": {
      "anyOf": [
        {
          "type": "string"
        },
        {
          "type": "null"
        }
      ],
      "default": null,
      "title": "Genbank"
    },
    "id": {
      "anyOf": [
        {
          "type": "string"
        },
        {
          "type": "null"
        }
      ],
      "default": null,
      "title": "Id"
    },
    "name": {
      "anyOf": [
        {
          "type": "string"
        },
        {
          "type": "null"
        }
      ],
      "default": null,
      "title": "Name"
    },
    "overwrite": {
      "default": false,
      "title": "Overwrite",
      "type": "boolean"
    },
    "seq": {
      "anyOf": [
        {
          "type": "string"
        },
        {
          "type": "null"
        }
      ],
      "default": null,
      "title": "Seq"
    },
    "topology": {
      "anyOf": [
        {
          "type": "string"
        },
        {
          "type": "null"
        }
      ],
      "default": null,
      "title": "Topology"
    },
    "type": {
      "title": "Type",
      "type": "string"
    }
  },
  "required": [
    "type"
  ],
  "title": "mitochondria_oligos_createArguments",
  "type": "object"
}

Output

{
  "properties": {
    "result": {
      "title": "Result",
      "type": "string"
    }
  },
  "required": [
    "result"
  ],
  "title": "mitochondria_oligos_createOutput",
  "type": "object"
}
GET/oligosPaged summaries for this key (id, type, name, topology, seq_length, has_genbank,

tool mitochondria_oligos_list

operationId oligos_list

Description

timestamps — not full seq/genbank). type filters insert, backbone, or construct

(invalid type: 422). limit default 50, clamped 0–100; offset default 0.

Envelope results: {items, total} where total is the unpaged count after type filter.

Input

{
  "properties": {
    "api_key": {
      "anyOf": [
        {
          "type": "string"
        },
        {
          "type": "null"
        }
      ],
      "default": null,
      "title": "Api Key"
    },
    "limit": {
      "default": 50,
      "title": "Limit",
      "type": "integer"
    },
    "offset": {
      "default": 0,
      "title": "Offset",
      "type": "integer"
    },
    "type": {
      "anyOf": [
        {
          "type": "string"
        },
        {
          "type": "null"
        }
      ],
      "default": null,
      "title": "Type"
    }
  },
  "title": "mitochondria_oligos_listArguments",
  "type": "object"
}

Output

{
  "properties": {
    "result": {
      "title": "Result",
      "type": "string"
    }
  },
  "required": [
    "result"
  ],
  "title": "mitochondria_oligos_listOutput",
  "type": "object"
}
GET/oligos/{id}Full oligo for this key, including seq and genbank when stored.

tool mitochondria_oligos_get

operationId oligos_get

Description

Missing or other-key ids: 404 (Not Found). Compute routes that load {id} and

miss a row return 422 instead.

Input

{
  "properties": {
    "api_key": {
      "anyOf": [
        {
          "type": "string"
        },
        {
          "type": "null"
        }
      ],
      "default": null,
      "title": "Api Key"
    },
    "id": {
      "title": "Id",
      "type": "string"
    }
  },
  "required": [
    "id"
  ],
  "title": "mitochondria_oligos_getArguments",
  "type": "object"
}

Output

{
  "properties": {
    "result": {
      "title": "Result",
      "type": "string"
    }
  },
  "required": [
    "result"
  ],
  "title": "mitochondria_oligos_getOutput",
  "type": "object"
}
DELETE/oligos/{id}Hard-deletes the oligo for this key and frees a storage slot. There is no undelete.

tool mitochondria_oligos_delete

operationId oligos_delete

Description

Missing or other-key ids: 404. Success results: {id} of the deleted oligo.

Input

{
  "properties": {
    "api_key": {
      "anyOf": [
        {
          "type": "string"
        },
        {
          "type": "null"
        }
      ],
      "default": null,
      "title": "Api Key"
    },
    "id": {
      "title": "Id",
      "type": "string"
    }
  },
  "required": [
    "id"
  ],
  "title": "mitochondria_oligos_deleteArguments",
  "type": "object"
}

Output

{
  "properties": {
    "result": {
      "title": "Result",
      "type": "string"
    }
  },
  "required": [
    "result"
  ],
  "title": "mitochondria_oligos_deleteOutput",
  "type": "object"
}
Catalog2 tools
GET/catalog/vectorsRead-only list of curated backbone vectors. Each item has name, description, and

tool mitochondria_catalog_vectors_list

operationId catalog_vectors_list

Description

length_bp. Currently includes pcDNA3.1. Catalog entries are not stored under the

API key; persist a copy with mitochondria_oligos_create when you need a reusable oligo.

Input

{
  "properties": {
    "api_key": {
      "anyOf": [
        {
          "type": "string"
        },
        {
          "type": "null"
        }
      ],
      "default": null,
      "title": "Api Key"
    }
  },
  "title": "mitochondria_catalog_vectors_listArguments",
  "type": "object"
}

Output

{
  "properties": {
    "result": {
      "title": "Result",
      "type": "string"
    }
  },
  "required": [
    "result"
  ],
  "title": "mitochondria_catalog_vectors_listOutput",
  "type": "object"
}
GET/catalog/vectors/{name}Returns catalog oligo: id, type "catalog", name, seq, genbank, topology, MCS

tool mitochondria_catalog_vector_get

operationId catalog_vector_get

Description

bounds. Pass {id, name, type: "catalog"} into cloning — do not paste seq/genbank

afterward. Never POST type catalog. Names case-sensitive; unknown: 404.

Input

{
  "properties": {
    "api_key": {
      "anyOf": [
        {
          "type": "string"
        },
        {
          "type": "null"
        }
      ],
      "default": null,
      "title": "Api Key"
    },
    "name": {
      "title": "Name",
      "type": "string"
    }
  },
  "required": [
    "name"
  ],
  "title": "mitochondria_catalog_vector_getArguments",
  "type": "object"
}

Output

{
  "properties": {
    "result": {
      "title": "Result",
      "type": "string"
    }
  },
  "required": [
    "result"
  ],
  "title": "mitochondria_catalog_vector_getOutput",
  "type": "object"
}

Same MCP catalog as https://api.nexio.bio/mcp-config; styling matches this app.