Cortexa research tool·genomics·ensembl

Ensembl Get Alignment

Get genomic alignments between species for a genomic region. Returns multiple alignments showing conserved sequences across species groups. Supports EPO and PECAN alignment methods for predefined species groups (mammals, primates, fish, birds, sauropsids). Useful for studying sequence conservation.

Livelast probed 2026-05-01 01:00Z· 1337msCortexa

Status

The most recent probe succeeded. Safe to call from the agent today.

Last probed: 1d ago
Last success: 1d ago
Last latency: 1337ms

Schema

JSON Schema the agent (or your API call) must match.

{
  "properties": {
    "compact": {
      "default": true,
      "description": "Compact output format",
      "type": "boolean"
    },
    "display_species_set": {
      "description": "Comma-separated list to filter which species to display in results (optional, e.g., 'mouse,rat')",
      "type": "string"
    },
    "method": {
      "default": "EPO",
      "description": "Alignment method: EPO (high quality multiple), EPO_EXTENDED (extended coverage), PECAN (low coverage)",
      "enum": [
        "EPO",
        "EPO_EXTENDED",
        "PECAN"
      ],
      "type": "string"
    },
    "region": {
      "description": "Genomic region in format 'chromosome:start-end' (e.g., '2:106000000-106100000')",
      "type": "string"
    },
    "species": {
      "description": "Source species (e.g., 'human', 'homo_sapiens')",
      "type": "string"
    },
    "species_set_group": {
      "default": "mammals",
      "description": "Predefined species group for multiple alignment. Options: 'mammals', 'primates', 'fish', 'birds', 'sauropsids'. Required for EPO method.",
      "type": "string"
    }
  },
  "required": [
    "species",
    "region"
  ],
  "type": "object"
}

Examples (1)

Default Ensembl Get Alignment call

public-safeinput

{
  "compact": false,
  "region": "",
  "species": ""
}

Expected response keys: success

Anonymous-safe example. Rate-limited; no sign-in required.

Identifiers

Catalog ID: tu_ensembl_get_alignment
Tool name: ensembl_get_alignment
Added: 2026-05-01 00:58Z
Tags: tooluniverse

Ensembl Get Alignment

Livelast probed 2026-05-01 01:00Z· 1337msCortexa

Schema

JSON Schema the agent (or your API call) must match.

{ "properties": { "compact": { "default": true, "description": "Compact output format", "type": "boolean" }, "display_species_set": { "description": "Comma-separated list to filter which species to display in results (optional, e.g., 'mouse,rat')", "type": "string" }, "method": { "default": "EPO", "description": "Alignment method: EPO (high quality multiple), EPO_EXTENDED (extended coverage), PECAN (low coverage)", "enum": [ "EPO", "EPO_EXTENDED", "PECAN" ], "type": "string" }, "region": { "description": "Genomic region in format 'chromosome:start-end' (e.g., '2:106000000-106100000')", "type": "string" }, "species": { "description": "Source species (e.g., 'human', 'homo_sapiens')", "type": "string" }, "species_set_group": { "default": "mammals", "description": "Predefined species group for multiple alignment. Options: 'mammals', 'primates', 'fish', 'birds', 'sauropsids'. Required for EPO method.", "type": "string" } }, "required": [ "species", "region" ], "type": "object" }