Look up genes, fetch sequences, predict variant consequences, find orthologs, and retrieve cross-database xrefs from Ensembl REST via MCP. STDIO or Streamable HTTP.
Setup
Choose your client, copy the config, then fill in any required environment variables.
Local
claude mcp add ensembl -- npx -y @cyanheads/ensembl-mcp-server~/.codex/config.toml
[mcp_servers.ensembl]
command = "npx"
args = ["-y", "@cyanheads/ensembl-mcp-server"]
# codex mcp add ensembl -- npx -y @cyanheads/ensembl-mcp-server~/.cursor/mcp.json
{
"mcpServers": {
"ensembl": {
"command": "npx",
"args": [
"-y",
"@cyanheads/ensembl-mcp-server"
]
}
}
}.vscode/mcp.json
{
"servers": {
"ensembl": {
"type": "stdio",
"command": "npx",
"args": [
"-y",
"@cyanheads/ensembl-mcp-server"
]
}
}
}~/.gemini/settings.json
{
"mcpServers": {
"ensembl": {
"command": "npx",
"args": [
"-y",
"@cyanheads/ensembl-mcp-server"
]
}
}
}claude_desktop_config.json
{
"mcpServers": {
"ensembl": {
"command": "npx",
"args": [
"-y",
"@cyanheads/ensembl-mcp-server"
]
}
}
}.trae/mcp.json
{
"mcpServers": {
"ensembl": {
"command": "npx",
"args": [
"-y",
"@cyanheads/ensembl-mcp-server"
]
}
}
}Remote
claude mcp add --transport http ensembl https://ensembl.caseyjhand.com/mcp~/.codex/config.toml
[mcp_servers.ensembl]
url = "https://ensembl.caseyjhand.com/mcp"
# codex mcp add ensembl --url https://ensembl.caseyjhand.com/mcp~/.cursor/mcp.json
{
"mcpServers": {
"ensembl": {
"url": "https://ensembl.caseyjhand.com/mcp"
}
}
}.vscode/mcp.json
{
"servers": {
"ensembl": {
"type": "http",
"url": "https://ensembl.caseyjhand.com/mcp"
}
}
}~/.gemini/settings.json
{
"mcpServers": {
"ensembl": {
"httpUrl": "https://ensembl.caseyjhand.com/mcp"
}
}
}claude_desktop_config.json · Customize › Connectors › Add custom connector
{
"mcpServers": {
"ensembl": {
"command": "npx",
"args": [
"-y",
"mcp-remote",
"https://ensembl.caseyjhand.com/mcp"
]
}
}
}.trae/mcp.json
{
"mcpServers": {
"ensembl": {
"url": "https://ensembl.caseyjhand.com/mcp"
}
}
}