"A tool for finding relevant files in a Git project based on questions" matching MCP servers:

Provides an MCP interface to the ROBOT command-line tool for OWL ontology editing, enabling operations like merging, reasoning, and conversion via natural language.

Enables genomic sequence analysis through the Evo 2 model, supporting DNA sequence scoring, embedding, generation, and variant effect prediction with multiple model checkpoints (7B, 40B, 1B parameters).

Enables variant annotation and effect prediction using the Ensembl VEP API, with support for batch and single queries.

This server enables multi-agent conversations for interacting with Cirro's biological data platform through its OpenAPI interface, auto-generated using AG2's MCP builder.

MCP server and Claude Plugin for a full ENCODE Project genomic data and analysis toolkit — search, download, track, and analyze functional genomics experiments

MCP server offering verified bioinformatics tools for sequence utilities and statistics, backed by BioPython/scipy. Enables AI agents to perform accurate GC content, translation, ORF finding, motif scanning, and statistical tests through natural language.

Provides access to EMBL-EBI bioinformatics data including InterPro domains, Pfam families, protein features, and taxonomy through a unified tool.

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.

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 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 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.

Enables querying the SymMap v2 Traditional Chinese Medicine association graph, covering herbs, ingredients, protein targets, symptoms, syndromes, and diseases with evidence-tiered relationships. It also supports plain-English questions through Pipeworx's ask_pipeworx meta-tool.

Access to 1000 Genomes Project dataset, hosted online in Dnaerys variant store

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.

MCP server for querying gene annotations, full-text gene search, and species taxonomy via MyGene.info. Enables AI agents to access gene data through natural language questions.

Enables querying of the Monarch Initiative biomedical knowledge graph for genes, diseases, phenotypes, and their associations through natural language or direct tool calls.

Federates 13 gene-related MCP backends (gnomAD, GTEx, etc.) behind a single Streamable HTTP endpoint with collision-free namespacing and search-based tool discovery.

🔍 A biomedical literature annotation and relationship mining server based on PubTator3, providing convenient access through the MCP interface.

Enables looking up genes, fetching sequences, predicting variant consequences, finding orthologs, and cross-database xrefs via Ensembl REST API through MCP.

Validates the physical and chemical plausibility of ligand–protein docking poses using the PoseBusters tool.