"A tool or assistant to explore and debug my codebase" 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.

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.

An MCP server that provides access to the Kyoto Encyclopedia of Genes and Genomes (KEGG) database, offering 30 tools for searching and analyzing biological data like pathways, genes, and compounds. It supports integration with LangChain and Ollama to enable LLMs to interact with comprehensive genomic and chemical datasets.

Enables AI agents to retrieve and analyze breeding data from BrAPI-compliant databases through shared tools, with human-in-the-loop approval and verification.

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.

Provides read-only access to the ProPaths verified protein interactome, letting AI agents search proteins, retrieve mechanistic interaction details, and explore pathway ontology through MCP tools, resources, and prompts.

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.

A bridge connecting AI agents to NCBI's PubMed database through the Model Context Protocol, enabling seamless searching, retrieval, and analysis of biomedical literature and data.

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

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.

A server that enables AI assistants to interact with cancer genomics data from cBioPortal, allowing users to explore cancer studies, access genomic data, and retrieve mutations and clinical information.

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

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

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.

Enables searching a manually curated database of stable macromolecular protein complexes by protein or complex name, gene, GO term, or biological process, and fetching individual records by accession to retrieve subunits with UniProt identifiers, biological roles, and stoichiometry. Complements UniProt, IntAct, and STRING, and can be used keyless over a hosted gateway endpoint or run locally over stdio.

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

This server provides access to InterPro protein family, domain, and functional-site classification data from EBI. It allows querying protein annotations through natural language or direct tool calls.