"A tool for searching local files and code" 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.

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

A production-ready Model Context Protocol (MCP) server that provides comprehensive access to the BioOntology API for searching, annotating, and exploring over 1,200 biological ontologies.

Enables users to generate volcano plots by submitting jobs with input files and parameters, supporting local or Docker execution.

Enables AI agents to search public cancer genomics studies (TCGA, CPTAC, MSK, and more), fetch full details for individual studies, resolve gene symbols to Entrez ids, and list cancer types. Works keylessly against open cBioPortal data over a hosted MCP endpoint, a local stdio server, or plain HTTP.

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 searching and retrieving cancer-genomics projects, cases, and genomic data files — including TCGA, TARGET, and CPTAC — via keyless, open-access metadata tools. Supports filtering by primary site, project, or data category, and can route plain-English questions to the right tool automatically.

Enables searching cancer genes and curated variants from CIViC, retrieving associated diseases, therapies, and graded evidence items and assertions for clinical interpretation.

Connects to NCBI E-utilities for searching, fetching, and linking biological data across Entrez databases.

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

Enables querying roughly 3.2 million measured protein–ligand binding affinities from a local, read-only DuckDB build of the BindingDB MySQL dump, with tools for searching compounds and targets, retrieving potency and selectivity profiles, fetching activity records with assay and citation details, and running read-only SQL.

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

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

Provides MCP tool adapters for Bioconductor methods like limma, DESeq2, and fgsea, enabling statistical analysis of omics data through containerized R execution. It serves as a bridge between MCP clients and bioinformatics tools for reproducible research workflows.

A specialized MCP server for Metal-Organic Framework research that provides tools for database searching, structural optimization, and energy calculations via ASE. It enables scientific workflows by allowing users to interact with MOF data and perform chemical simulations through a standard SSE interface.

A local-first MCP server that annotates whole-genome VCF files and lets you query pharmacogenomics, disease risk, and carrier status through natural language.

A server providing access to NCBI E-utilities API for searching and retrieving data from databases like PubMed, Protein, and Nucleotide.