"Guidance on Dependency Checks and Latest Best Practices" matching MCP servers:

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.

Enables AI-driven pharmacogenomic analysis by querying structured genetic variant, drug response, and disease risk data. Supports natural language questions about medications, traits, and health risks based on user genome data, with privacy-first local execution.

Enables Claude Desktop to read and drive analyses on the active MilliMap session, including datasets, clusters, annotations, and markers.

Leverages large language models to analyze users' WeGene genetic testing reports, providing access to report data via custom URI schemes and enabling profile and report management through OAuth authentication and API utilization.

MCP server providing access to the BERtron API for aggregating genomic and environmental data from multiple BER data sources, enabling geospatial search and health checks.

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.

Enables users to manage and navigate nf-core bioinformatics pipeline repositories, allowing list, search, and explore operations on pipeline configurations, workflows, and modules.

Enables querying and accessing hivtools data through a REST API and MCP-compatible tools.

Agent-callable canine genomics API providing breed-stratified allele frequencies, pathogenicity predictions, and variant-gene-breed-disease knowledge graph for dog DNA.

Bridge any AI coding assistant directly to GenePattern — run bioinformatics modules, manage cloud jobs, and stream results, all through natural language.

Enables AI assistants to perform quality control analysis on high-throughput sequencing data using FastQC and MultiQC. It supports single-file and batch processing of FASTQ/FASTA files and generates comprehensive, interactive summary reports.

MCP server for interacting with Galaxy bioinformatics platform, enabling AI assistants to connect to Galaxy instances, search and execute tools, manage workflows, and access other features.

Enables querying the gnomAD genome aggregation database for variant, gene, and region information.

Enables molecular generation, optimization, and analysis through NVIDIA MolMIM API. Supports generating drug-like molecules with desired properties, extracting molecular embeddings, and exploring chemical space around seed molecules.

MCP-native scientific skills for reproducible computational biology and AI-driven drug-discovery workflows. It combines deterministic scientific tools with an MCP server to give AI agents real computational capabilities.

Provides access to BioThings.io APIs for comprehensive gene and variant annotations, enabling seamless integration of biological data into workflows.

MCP server for querying the GWAS Catalog (EBI/NHGRI), a curated catalog of genome-wide association studies. It enables AI agents to search and retrieve study data via natural language or direct tool calls.

Exposes pipen bioinformatics pipelines as MCP tools, allowing AI assistants to discover and run complex workflows through a progressive disclosure interface.

Enables AI agents to query the PomBase fission yeast model-organism database for genetic and molecular data through the Pipeworx MCP gateway.

Enables AI agents to read and manipulate networks, tables, visual styles, and more in a live Cytoscape Web session through natural language, by connecting over Chrome DevTools Protocol.