Ensembl MCP Server

Name: Ensembl MCP Server
Author: cyanheads

作者：cyanheads版本 0.7.1i★ –i电脑或云端

注册名称io.github.cyanheads/ensembl-mcp-server

安装

概览

作者提供的说明（英文原文）

Look up genes, sequences, variants, homologs, and cross-database xrefs from Ensembl REST.

PopNx MCP 的三大支柱

这三项永远不会合并成一个分数：意见、测量和人气是不同的东西。

用户评价i暂无评价评价功能将在后续阶段与账户功能一起开放
我们的基础检查i3 项中通过 3 项依据公开信息检查；尚未扫描代码
使用情况i非常新↓ 164/周 · ★ –

它能帮你做什么

我们还没有为它写通俗的介绍。下面是我们从注册中心读取到的事实。

连接方式: 电脑或云端
传输方式: stdio, Streamable HTTP
分类: 数据库与数据集

安装

选择你使用的 AI 应用，然后复制设置。

安装之前

基础检查：3 项中通过 3 项
在作者的服务器上运行：你向它提出的内容会经过他们的服务器。
可以做 7 件事（工具） ensembl_list_species, ensembl_lookup_gene, ensembl_get_sequence, ensembl_query_region …
需要你自己填写： ENSEMBL_BASE_URL, MCP_LOG_LEVEL

你需要

在云端运行无需安装任何东西，通过互联网连接
npm已安装 Node.js（用于 npx 命令）

你用的是哪个应用？

ClaudeClaude CodeCursorVS CodeChatGPT

在上方选择你的应用。我们会记住它，下次按钮会显示“安装到 …”。

适用于网页版、桌面版和手机版 Claude：

打开 Settings → Connectors
点击 Add custom connector
粘贴下面的地址，然后点击 Add
如果要求登录，请登录作者的服务

https://ensembl.caseyjhand.com/mcp

或者在你的电脑上运行

打开 Claude Desktop → Settings → Developer → Edit Config，把下面的内容粘贴到 claude_desktop_config.json

{
  "mcpServers": {
    "ensembl": {
      "command": "npx",
      "args": [
        "-y",
        "@cyanheads/ensembl-mcp-server"
      ],
      "env": {
        "ENSEMBL_BASE_URL": "your-value",
        "MCP_LOG_LEVEL": "your-value"
      }
    }
  }
}

在终端中运行这条命令

claude mcp add --transport http ensembl https://ensembl.caseyjhand.com/mcp

或者在你的电脑上运行

claude mcp add ensembl --env ENSEMBL_BASE_URL=your-value --env MCP_LOG_LEVEL=your-value -- npx -y @cyanheads/ensembl-mcp-server

运行前请先填写空着的值。

在 Cursor 中打开

或者自己复制设置

粘贴到项目中的 .cursor/mcp.json，或 ~/.cursor/mcp.json

{
  "mcpServers": {
    "ensembl": {
      "url": "https://ensembl.caseyjhand.com/mcp"
    }
  }
}

或者在你的电脑上运行

在 Cursor 中打开

或者自己复制设置

粘贴到项目中的 .cursor/mcp.json，或 ~/.cursor/mcp.json

{
  "mcpServers": {
    "ensembl": {
      "command": "npx",
      "args": [
        "-y",
        "@cyanheads/ensembl-mcp-server"
      ],
      "env": {
        "ENSEMBL_BASE_URL": "your-value",
        "MCP_LOG_LEVEL": "your-value"
      }
    }
  }
}

浏览器会先询问是否打开应用，然后应用会显示设置并请你确认。密钥的值会留空，由你自己填写。

在 VS Code 中打开

或者自己复制设置

粘贴到项目中的 .vscode/mcp.json

{
  "servers": {
    "ensembl": {
      "type": "http",
      "url": "https://ensembl.caseyjhand.com/mcp"
    }
  }
}

或者在你的电脑上运行

在 VS Code 中打开

或者自己复制设置

粘贴到项目中的 .vscode/mcp.json

{
  "servers": {
    "ensembl": {
      "type": "stdio",
      "command": "npx",
      "args": [
        "-y",
        "@cyanheads/ensembl-mcp-server"
      ],
      "env": {
        "ENSEMBL_BASE_URL": "your-value",
        "MCP_LOG_LEVEL": "your-value"
      }
    }
  }
}

浏览器会先询问是否打开应用，然后应用会显示设置并请你确认。密钥的值会留空，由你自己填写。

ChatGPT 只能连接互联网上的服务器：

打开网页版 ChatGPT → Settings → Connectors (Apps)
点击 Create 或 Add（部分套餐需要先在 Advanced 中开启 Developer mode）
粘贴下面的地址，起个名字，然后保存
如果要求登录，请登录作者的服务

https://ensembl.caseyjhand.com/mcp

菜单名称可能因套餐和版本不同而略有差异。

你的选择通过 Cookie 保存在这台设备上，无需账户。

需要你填写的值

ENSEMBL_BASE_URL env
Ensembl REST API base URL. Override to use GRCh37 endpoint or a local mirror.
MCP_LOG_LEVEL env
Sets the minimum log level for output (e.g., 'debug', 'info', 'warn').

这些设置是根据作者在注册中心的条目生成的。如果 README 的写法不同，请以 README 为准。

它能做什么

工具名称和描述与服务器在 2026年11月7日报告的完全一致。这些内容由作者撰写，不是我们写的；我们以纯文本形式显示。

ensembl_list_species
List species supported by Ensembl with display name, common name, assembly, taxon ID, and division. Required discovery step — species names like homo_sapiens are opaque to non-biologists and are the input format every other Ensembl tool expects. Use nameContains to find a species
ensembl_lookup_gene
Resolve a gene by symbol + species (or by stable ID) to its Ensembl ID, genomic location (chr:start-end:strand), biotype, description, and transcript list. Entry point for most workflows — the stable ID and coordinates returned here are inputs to other tools. Accepts both symbol
ensembl_get_sequence
Fetch the DNA, cDNA, CDS, or protein sequence for a gene, transcript, protein, or genomic region. Returns a window of the sequence — the first 10,000 characters by default — with its stable ID, molecule type, and full length. When more follows the window, truncated is true and ne
ensembl_query_region
Find genomic features overlapping a chromosomal region: genes, transcripts, variants, regulatory elements, or exons. Returns each feature with its stable ID, type, location, biotype, and name, plus the genome assembly the coordinates are on. Useful for "what's in this locus?" and
ensembl_predict_variant
Predict the functional consequences of a sequence variant using the Ensembl Variant Effect Predictor (VEP). Accepts three input formats: HGVS notation (transcript-relative, e.g. ENST00000380152.8:c.2T>A, or genomic, e.g. 13:g.32316462T>A); region+allele (chr:start:end:strand/alle
ensembl_get_homology
Find orthologs and/or paralogs of a gene across species. Returns each homolog's stable ID, species, homology type (ortholog_one2one, ortholog_one2many, paralog_many2many, etc.), percId and percPos (percent identical and positive positions, over the target protein's length), and t
ensembl_get_xrefs
Retrieve cross-database references for a gene or feature — HGNC, UniProt, EntrezGene, OMIM, RefSeq, Reactome, and others. Returns each xref with its database name, primary ID, display ID, and description, plus how Ensembl assigned it (infoType, infoText) and its evidence codes (l

基础检查i

我们检查的是任何人都能看到的信息；我们没有阅读代码。不适用的检查项不计入总数。 · 检查于 2026年11月8日

✓ 通过
作者与仓库一致
注册名称已通过 GitHub 账户 cyanheads 验证，该账户拥有此仓库
… 尚未检查
仍在维护
我们还没有从 GitHub 读取这个仓库
… 尚未检查
有许可证
我们还没有从 GitHub 读取这个仓库
✓ 通过
端点有响应
在 498 毫秒内响应（HTTP 200）
– 不适用
使用 OAuth 登录
无需登录
✓ 通过
工具描述中没有隐藏指令
已读取 7 个工具描述，未发现针对 AI 的隐藏指令

与“数据库与数据集”中的其他服务器比较i

星标数多于此分类中其他 1146 个服务器的 0%
发布到注册中心的时间比此分类中其他 1146 个服务器的 77% 更新
基础检查结果等于或优于此分类中其他 1146 个服务器的 100%

与注册中心里这个分类中所有活跃的服务器比较。只有当发布者拥有该仓库时，星标数才计入。

常见问题

Ensembl MCP Server 安全吗？

它在 3 项适用的基础检查中通过了 3 项。我们没有阅读代码。在添加密钥或令牌之前，请先看看这个服务器要求哪些权限，并使用只具备所需权限的密钥。

它需要哪些密钥或代码？

注册中心没有列出必需的密钥，不过有些服务器会在首次使用时要求你登录。

它在我的电脑上运行还是在云端？

两种方式都可以：安装在你的电脑上，或者连接云端版本。

它还在维护吗？

GitHub 仓库最后更新于–，最新版本（0.7.1）于10天前进入注册中心。

哪些应用可以使用它？

支持 MCP 的应用，例如 Claude Desktop、Claude Code、Cursor 和 VS Code。它通过 URL 连接，所以接受远程 MCP 服务器的应用也可以使用，例如开启开发者模式的 ChatGPT。

有什么可以替代它？

同一分类中有：Supabase, MongoDB MCP Server, Elasticsearch MCP Server

替代选择

同一分类中其他作者的服务器，按星标数排序。

如何看卡片：↓ 每周下载量i★ GitHub 星标i三大支柱：评价 · 检查 · 使用情况i更新 = 最新版本发布到注册中心的时间i

Supabase

MCP server for interacting with the Supabase platform

作者：supabase广泛使用↓ 23.5万/周★ 2993前天更新

电脑或云端✓ supabase.com

安装

MongoDB MCP Server

MongoDB Model Context Protocol Server

作者：mongodb-js广泛使用↓ 15.7万/周★ 11574天前更新

在你的电脑上运行

安装

Elasticsearch MCP Server

MCP server for interacting with Elasticsearch

作者：cr7258正在增长↓ 2711/周★ 31514个月前更新

在你的电脑上运行

安装

作者的 README

打开 README

按原文从作者的仓库复制。PopNx MCP 没有审查或背书其内容。HTML、图片和脚本已被移除。链接会离开本站。

@cyanheads/ensembl-mcp-server Look up genes, fetch sequences, predict variant consequences, find orthologs, and retrieve cross-database xrefs from Ensembl REST via MCP. STDIO or Streamable HTTP. 7 Tools • 4 Resources • 1 Prompt

Public Hosted Server: https://ensembl.caseyjhand.com/mcp

Overview

Gene, sequence, and variant data for vertebrates and other model organisms from the Ensembl REST API. Look up genes, fetch sequences, predict variant consequences, find orthologs, and cross-reference external databases.

Tools

Tool	Description
`ensembl_list_species`	List species supported by Ensembl with display name, common name, assembly, taxon ID, and division
`ensembl_lookup_gene`	Resolve a gene by symbol (synonyms and former symbols included) + species or by stable ID to its Ensembl ID, genomic location, biotype, and transcript list
`ensembl_get_sequence`	Fetch the DNA, cDNA, CDS, or protein sequence for a gene, transcript, protein, or genomic region
`ensembl_query_region`	Find genomic features (genes, transcripts, variants, regulatory elements, exons) overlapping a chromosomal region
`ensembl_predict_variant`	Predict functional consequences of a sequence variant using the Ensembl Variant Effect Predictor (VEP)
`ensembl_get_homology`	Find orthologs and/or paralogs of a gene across species with percent identity and taxonomy level
`ensembl_get_xrefs`	Retrieve cross-database references for a gene — HGNC, UniProt, EntrezGene, OMIM, RefSeq, Reactome, and others

Resources

Resource	Description
`ensembl://gene/{id}`	Gene record by stable ID (`ENSG…`) — location, biotype, description, and transcript list
`ensembl://transcript/{id}`	Transcript record by stable ID (`ENST…`) — parent gene, location, biotype, canonical flag, and length
`ensembl://species`	Supported Ensembl species for the endpoint default division (vertebrates on the default endpoint)
`ensembl://species/{division}`	Supported species in one division (`EnsemblVertebrates`, `EnsemblPlants`, `EnsemblFungi`, `EnsemblMetazoa`, `EnsemblProtists`)

The species resources return the first 50 species by internal name; the ensembl_list_species tool pages through the rest and filters by name.

Prompts

Prompt	Description
`ensembl_gene_dossier`	Structured workflow for assembling a complete gene profile: symbol → ID + location → sequence → variants → orthologs → xrefs

Capability reference

Ensembl's stable-ID endpoints answer a versioned ID (ENSG00000139618.19) as not found, so every tool and resource that takes an Ensembl stable ID drops a trailing .N from an ENS… ID before the request and returns the current version. HGVS input to ensembl_predict_variant (ENST00000380152.8:c.2T>A) keeps its version, and IDs from other sources (AT3G52430.1) are forwarded unchanged.

`ensembl_list_species` tool

Optional division (EnsemblVertebrates, EnsemblPlants, EnsemblFungi, EnsemblMetazoa, EnsemblProtists; omitted, the endpoint default — vertebrates, ~356 species on GRCh38) and nameContains, a substring match against name, display name, and common name
Returns the internal name every other tool expects (homo_sapiens), plus display name, common name, taxon ID, assembly, and division
Sorted by internal name and paged by offset (default 0) and max_results (default 50, 0 uncapped); totalCount reports every match, and nextOffset is where the next page starts when more follow

`ensembl_lookup_gene` tool

Exactly one of symbol (+ species, default homo_sapiens), id, ids, or symbols (up to 1,000 submitted items; first 20 distinct trimmed queries processed); expand_transcripts (default false) adds the transcript list with biotype and canonical flag
canonicalTranscript identifies the canonical transcript without expansion; transcript-ID lookups also return parentGeneId. Expanded transcripts include maneSelect RefSeq accessions when available (BRCA2: ENST00000380152.8, NM_000059.4)
A symbol that is not a current gene name falls back to synonyms and former symbols (HER2 → ERBB2), reported as matchedAlias; a name shared by several genes (MDR1) returns ambiguous with candidates to retry by id
A single lookup returns gene (or ambiguous); a batch returns ordered succeeded items carrying the submitted query, failed items with query, reason (not_found, ambiguous with candidates, or unavailable), error, and recovery, and omitted queries past the processing cap. Omitted queries are never requested or reported as failed; resubmit them separately. Errors: not_found, invalid_species, no_input, conflicting_input

`ensembl_get_sequence` tool

A stable ID (ENSG…/ENST…/ENSP…) or a region (species:chr:start-end, or chr:start-end with species; at most 10,000,000 bases); type is genomic (default), cdna, cds, or protein — cdna and cds from a transcript ID only, protein from a transcript or protein ID; expand_5prime/expand_3prime add flanking bases
Regions take a :1/:-1 strand suffix (1:1000000-1000020:-1 returns the reverse complement); the mitochondrion is MT in vertebrates (mitochondrion_genome in Drosophila, MtDNA in C. elegans), and M/chrM are rejected as invalid_region where they would not resolve to it
Returns a window set by offset (default 0) and max_length (default 10000, 0 uncapped); length is the full sequence length, and truncated/nextOffset say where to resume
Errors: not_found, type_mismatch (also a protein ID asked for genomic/cdna/cds, or a non-coding transcript asked for protein/cds), invalid_species, missing_species, invalid_region (also an id with a colon that is not a valid region)

`ensembl_query_region` tool

region as species:chr:start-end, or chr:start-end with species (at most 5,000,000 bases; reversed coordinates are rejected; mitochondrion naming as in ensembl_get_sequence); feature defaults to ["gene"] and also accepts transcript, variation, regulatory, exon; optional case-sensitive biotype filter (protein_coding, lncRNA). An empty filtered result suggests removing the filter without inferring the locus is intergenic
max_results caps the list (default 100, 0 uncapped) while totalCount reports the true count; assemblyName names the coordinates' assembly, and exon rows carry parentId and rank. Errors: invalid_region, invalid_species, missing_species

`ensembl_predict_variant` tool

variant as HGVS (transcript-relative or genomic), region+allele (chr:start:end:strand/allele), or a dbSNP rsID
Returns the most severe consequence, per-transcript impact (HIGH/MODERATE/LOW/MODIFIER), and colocated known variants with clinical significance. Errors: invalid_notation, not_found, invalid_species
Requests HGVS, canonical and MANE annotations on every input route. Consequences retain variantAllele, optional canonical/maneSelect, HGVS and available SIFT/PolyPhen prediction-score pairs; records retain alleleString
Colocated clinicalSignificance is aggregate, not a classification of the submitted allele. clinicalSignificanceByAllele preserves explicit per-allele terms and clinicalSignificanceReferenceAllele identifies their reference allele; absent annotations remain omitted
max_transcript_consequences and max_pubmed_ids_per_variant (default 10 each, 0 uncapped; include_all_colocated_pubmed lifts the PubMed cap) bound the result, while transcriptConsequencesTotal and pubmedTotal report the full counts

`ensembl_get_homology` tool

Exactly one of symbol (+ species, default homo_sapiens) or id; type is orthologues (default), paralogues, or all; optional target_species filter
A target_species outside the comparison Ensembl runs for the source species (a fly gene to homo_sapiens) is answered from Ensembl's pan-taxonomic comparison when it holds both species, with a notice saying so
max_results caps the list (default 25, 0 uncapped) while totalCount reports the true count. Errors: not_found, invalid_species (unknown species or target_species), target_not_compared (a target outside the source species' comparison that the pan-taxonomic comparison cannot answer), no_input, conflicting_input
Each row retains optional targetProteinId for ensembl_get_sequence with type:"protein". Optional targetSymbol comes from a lookup of the returned rows' distinct gene IDs, in chunks of at most 1,000, with one five-second budget bounded by the call's remaining deadline and no retries. Missing names or failed lookups retain every primary homolog with a notice; cancellation still aborts

`ensembl_get_xrefs` tool

id (ENSG…/ENST…/ENSP…) required; optional dbname filter (e.g. HGNC, Uniprot_gn, Uniprot/SWISSPROT for the reviewed UniProt accession on the translation, EntrezGene, MIM_GENE, RefSeq_mRNA, Reactome_gene for gene pathways, Reactome for translation pathways, GO)
Default all_levels:false queries the requested object's level. Set all_levels:true to include a gene's transcript and translation references, independently of dbname; for example, gene-level RefSeq_mRNA may need this or a transcript ID. Empty lists remain successful with totalCount:0. Errors: not_found
Each reference carries how Ensembl assigned it (infoType: DIRECT, DEPENDENT, PROJECTION, …; infoText: its source, such as UniProt or the ortholog a projection came from) and its evidence codes (linkageTypes, GO evidence such as IDA or IEA) when su

只显示了开头部分；其余内容请在仓库中阅读

Ensembl MCP Server

概览

PopNx MCP 的三大支柱

它能帮你做什么

安装

安装之前

或者在你的电脑上运行

或者在你的电脑上运行

或者在你的电脑上运行

或者在你的电脑上运行

需要你填写的值

它能做什么

基础检查i

作者与仓库一致

仍在维护

有许可证

端点有响应

使用 OAuth 登录

工具描述中没有隐藏指令

与“数据库与数据集”中的其他服务器比较i

常见问题

替代选择

Supabase

MongoDB MCP Server

Elasticsearch MCP Server

作者的 README

Overview

Tools

Resources

Prompts

Capability reference

ensembl_list_species tool

ensembl_lookup_gene tool

ensembl_get_sequence tool

ensembl_query_region tool

ensembl_predict_variant tool

ensembl_get_homology tool

ensembl_get_xrefs tool

`ensembl_list_species` tool

`ensembl_lookup_gene` tool

`ensembl_get_sequence` tool

`ensembl_query_region` tool

`ensembl_predict_variant` tool

`ensembl_get_homology` tool

`ensembl_get_xrefs` tool