Bioinformatics

Tools for computational analysis of biological data, including genomics, proteomics, and other molecular biology data. Enables access to bioinformatics pipelines, algorithms, and databases.

MCP ServersBrowse all →

BioContextAI Knowledgebase MCPofficial
Bioinformatics Autonomous Agents Research & Data
biocontext-ai
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license
A
quality
B
maintenance
An MCP server that provides standardized access to biomedical knowledge bases and resources, enabling AI systems to retrieve verified information from sources like bioRxiv, EuropePMC, and various protein/gene databases.
Last updated 2026-01-12
52
22
Apache 2.0
WormBase MCP Serverofficial
Bioinformatics Research & Data Biology & Medicine
WormBase
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license
A
quality
C
maintenance
Enables querying the WormBase database for C. elegans and nematode genomics data, including gene information, protein sequences, phenotypes, interactions, and expression patterns through natural language.
Last updated 2025-12-12
12
3
MIT
millimap-mcpofficial
Bioinformatics Research & Data Local
milliomics
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license
A
quality
C
maintenance
Enables Claude Desktop to read and drive analyses on the active MilliMap session, including datasets, clusters, annotations, and markers.
Last updated 2026-05-12
12
MIT
Noctua MCP Serverofficial
Biology & Medicine Research & Data Bioinformatics
geneontology
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license
A
quality
B
maintenance
Enables editing and querying of Gene Ontology Causal Activity Models (GO-CAMs) through the Barista API. Supports model creation, individual and fact management, evidence addition, and causal pathway construction for biological knowledge representation.
Last updated 2025-11-01
18
BSD 3-Clause
STRING-MCP
Bioinformatics Research & Data Biology & Medicine
MCPmed
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license
B
quality
C
maintenance
A Model Context Protocol server that provides tools for interacting with the STRING database to analyze protein-protein interaction networks and functional enrichment. It enables users to map protein identifiers, retrieve interaction data, and generate biological network visualizations through natural language interfaces.
Last updated 2025-07-28
11
3
BSD 3-Clause
Ensembl MCP Server
Autonomous Agents Bioinformatics Research & Data
effieklimi
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license
A
quality
C
maintenance
A Model Context Protocol server providing LLMs with access to the Ensembl genomics database, enabling AI assistants to query gene information, sequences, variants, and other genomic data across multiple species.
Last updated 2026-02-11
10
6
JavaScript
MIT
Protein MCP Server
Bioinformatics Research & Data Biology & Medicine
gqy20
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license
B
quality
C
maintenance
Enables searching, retrieving, and downloading protein structure data from the RCSB Protein Data Bank. Supports intelligent protein structure search, comprehensive data retrieval, and multiple file format downloads for bioinformatics research.
Last updated 2025-10-24
3
MIT
MCP-Slicer
Code Execution Bioinformatics App Automation
zhaoyouj
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license
A
quality
C
maintenance
Connects 3D Slicer with AI assistants through the Model Context Protocol, enabling medical image processing and scene manipulation using natural language.
Last updated 2025-11-05
3
31
MIT
AlphaGenome MCP Server
Bioinformatics Biology & Medicine Research & Data
taehojo
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license
B
quality
C
maintenance
Enables AI-powered genomic variant analysis including variant impact prediction, regulatory element discovery, and batch variant scoring. Currently operates in mock mode as a proof-of-concept awaiting the public release of Google DeepMind's AlphaGenome API.
Last updated 2026-03-03
20
29
2
MIT
MCP Sequence Simulation Server
Bioinformatics Research & Data Biology & Medicine
coreymhudson
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license
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quality
C
maintenance
Enables the generation, mutation, and evolution of DNA and protein sequences using various evolutionary models and phylogenetic algorithms. It supports realistic next-generation sequencing read simulation and population-level evolutionary tracking for bioinformatics research and testing.
Last updated 2025-06-17
6
BSD 2-Clause "Simplified"
clinicaltrialsgov-mcp-server
Bioinformatics Biology & Medicine Research & Data
cyanheads
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license
A
quality
B
maintenance
Empowers AI agents with direct access to the official ClinicalTrials.gov database, enabling programmatic searching, retrieval, and analysis of clinical study data through a Model Context Protocol interface.
Last updated 2026-05-10
7
2,982
70
Enrichr MCP Server
Bioinformatics Research & Data Biology & Medicine
tianqitang1
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license
A
quality
B
maintenance
Enables gene set enrichment analysis using the Enrichr API across hundreds of gene set libraries including Gene Ontology, pathways, diseases, tissues, drugs, and transcription factors. Returns only statistically significant results for interpretation.
Last updated 2026-04-07
2
83
14
MIT
Ensembl MCP Server
Bioinformatics Research & Data Biology & Medicine
munch-group
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license
B
quality
C
maintenance
Provides access to the Ensembl genomics REST API with 30+ tools for genomic data including gene lookup, sequence retrieval, genetic variants, cross-species homology, phenotypes, and regulatory features.
Last updated 2025-12-09
25
ISC
OpenGenes MCP Server
Research & Data Databases Bioinformatics
longevity-genie
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license
B
quality
C
maintenance
Provides standardized access to aging and longevity research data from the OpenGenes database, enabling AI assistants to query comprehensive biomedical datasets through SQL and structured interfaces.
Last updated 2025-10-14
3
17
MIT
UniProt MCP Server
Bioinformatics Research & Data Databases
josefdc
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license
B
quality
C
maintenance
Provides seamless access to UniProtKB protein database, enabling queries for protein entries, sequences, Gene Ontology annotations, full-text search, and ID mapping across 200+ database types.
Last updated 2026-03-02
5
2
MIT
Unofficial PubChem MCP Server
Research & Data Bioinformatics Remote
Augmented-Nature
F
license
B
quality
D
maintenance
A comprehensive Model Context Protocol server providing access to over 110 million chemical compounds with extensive molecular properties, bioassay data, and chemical informatics tools from the PubChem database.
Last updated 2025-12-21
1,452
30
36
Biomart MCP
Bioinformatics Databases Search
jzinno
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license
A
quality
C
maintenance
A Model Context Protocol server that interfaces with Biomart databases, allowing models to discover biological datasets, explore attributes/filters, retrieve biological data, and translate between different biological identifiers.
Last updated 2025-05-21
8
7
MIT
PubChem MCP Server
Research & Data Biology & Medicine Bioinformatics
k-lordbodin7
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license
B
quality
C
maintenance
Enables comprehensive access to PubChem's chemical database with over 110 million compounds. Supports chemical searches, structure analysis, bioactivity data, safety information, and molecular property calculations through 30 specialized tools.
Last updated 2025-09-29
30
MIT
UCSC Genome Browser MCP Server
Bioinformatics Research & Data Biology & Medicine
hlydecker
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license
B
quality
C
maintenance
Provides comprehensive access to the UCSC Genome Browser API, enabling queries of genomic data, DNA sequences, gene annotations, variants, and metadata across multiple species and assemblies.
Last updated 2025-11-13
12
3
MIT
MCP PubMed Search
Research & Data Search Bioinformatics
wavelovey
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license
B
quality
C
maintenance
Server to search PubMed (PubMed is a free, online database that allows users to search for biomedical and life sciences literature). I have created on a day MCP came out but was on vacation, I saw someone post similar server in your DB, but figured to post mine.
Last updated 2024-12-12
1
47
MIT
BioPython MCP Server
Bioinformatics Research & Data Hybrid
kmaneesh
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license
B
quality
B
maintenance
Provides comprehensive BioPython capabilities for biological sequence analysis, alignment, database access (GenBank, UniProt, PubMed), protein structure analysis, and phylogenetics through a Model Context Protocol interface for AI-assisted bioinformatics workflows.
Last updated 2026-01-16
32
2
MIT
gnomAD MCP Server
Bioinformatics Research & Data Biology & Medicine
koido
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license
B
quality
B
maintenance
Provides a programmatic interface to the Genome Aggregation Database (gnomAD) API across versions v2.1.1, v3.1.2, and v4.1.0. It enables users to query gene metadata, variant information, population frequencies, and ClinVar data through a unified schema.
Last updated 2026-01-23
12
5
Apache 2.0
pubmed-mcp-server
Research & Data Bioinformatics Hybrid
AIAnytime
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license
B
quality
D
maintenance
Search PubMed for articles matching the query.
Last updated 2026-05-04
1
61
MIT
genome-mcp
Bioinformatics Research & Data Biology & Medicine
gqy20
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license
B
quality
B
maintenance
Intelligent Genomic Data Server Provides high-quality gene information queries, homologous gene analysis, and evolutionary research functions via the MCP protocol.
Last updated 2025-12-08
6
2
MIT
UniProt MCP Server
Bioinformatics Research & Data Databases
TakumiY235
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license
B
quality
C
maintenance
Enables AI assistants to access protein information directly from UniProt, allowing retrieval of protein names, functions, sequences, and organism data by accession number.
Last updated 2025-03-11
2
11
MIT
STRING MCP Server
Bioinformatics Research & Data Biology & Medicine
munch-group
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license
B
quality
C
maintenance
Provides access to the STRING protein-protein interaction database for mapping identifiers, retrieving interaction networks, and performing functional enrichment analysis. It enables users to explore protein partners, pathways, and cross-species homology through natural language interactions.
Last updated 2025-12-09
9
ISC
encode-toolkit
Biology & Medicine Bioinformatics Research & Data
ammawla
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license
A
quality
B
maintenance
MCP server and Claude Plugin for a full ENCODE Project genomic data and analysis toolkit — search, download, track, and analyze functional genomics experiments
Last updated 2026-05-08
20
34
7
AGPL 3.0
ChatSpatial
Biology & Medicine Research & Data Bioinformatics
cafferychen777
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license
A
quality
A
maintenance
Natural language-driven spatial transcriptomics analysis via MCP. Integrates 60+ methods for preprocessing, visualization, spatial statistics, cell communication, deconvolution, and trajectory analysis.
Last updated 2026-05-12
20
36
MIT
Omics AI MCP Server
Bioinformatics Research & Data Databases
mfiume
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license
A
quality
C
maintenance
Enables AI agents to conversationally interact with genomics research networks for data analysis and discovery across multiple Omics AI Explorer platforms. It provides tools for exploring data collections, examining table schemas, and executing SQL queries against datasets like Viral AI and Neuroscience AI.
Last updated 2025-06-20
6
1
MIT
Rowan MCP Server
Biology & Medicine Research & Data Bioinformatics
k-yenko
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license
B
quality
D
maintenance
Enables molecular design and simulation through 45 chemistry tools including pKa calculations, geometry optimization, conformer searches, docking, protein cofolding, and ADMET predictions powered by Rowan's computational chemistry platform.
Last updated 2025-11-18
41
23
MIT

MCP ConnectorsBrowse all →

BioBTreeA
A unified biomedical graph database that integrates 50+ primary data sources — genes, proteins, compounds, diseases, pathways, and clinical data — into a single queryable graph with billions of cross-reference edges. Its native MCP server gives LLMs direct access to structured, authoritative biomedical data, complementing their reasoning with reliable identifiers and up-to-date database content.
Bioinformatics Databases Research & Data
31
phasefolioA
Biotech rNPV/PoS engine for AI agents. Signed exports, evidence register, asset landscape.
Bioinformatics Finance AI & Machine Learning
91
Arquestra — Scientific Computing Orchestration
AI orchestration for computational chemistry and HPC workflows.
Bioinformatics AI & Machine Learning
1
mcp
Gencove consumer genomics: profile, kit status, ancestry, PRS, raw data. Requires Gencove auth.
Biology & Medicine Bioinformatics
1
PatSnap Biology Modality
PatSnap Biology Modality MCP server — access biological sequences, modification records, and antibody-antigen interactions across 200M+ patents.
Biology & Medicine Bioinformatics
1

Bioinformatics

MCP ServersBrowse all →

BioContextAI Knowledgebase MCPofficial

WormBase MCP Serverofficial

millimap-mcpofficial

Noctua MCP Serverofficial

MCP ConnectorsBrowse all →