"Rewriting or modifying Debian packages" matching MCP servers:

An MCP server that gives Claude access to NCBI Datasets v2 — search genome assembly metadata, retrieve taxonomy records, and download data packages without leaving your conversation.

Enables language models to search biomedical literature, fetch sequences, and follow links across Entrez databases through eleven read-only tools wrapping the nine NCBI Entrez E-utilities. It handles URL building, pacing, redirects, response caps, and API-key redaction so queries can be answered without a browser or scraping.

Enables AI assistants to clean PDB structures and run initial-stage energy relaxation for biomolecular modeling. It provides a structured workflow for preparing structures before production molecular dynamics or coarse-graining pipelines.

Enables MCP clients to annotate and classify single human genetic variants in any notation, returning an auditable points-based ACMG verdict with its criteria, gnomAD frequencies, in-silico predictors, ClinVar data, and per-transcript consequences. It is read-only, requires no account or API key, and keeps answers compact while linking back to the source.

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.

Enables agents to search a public PubMed-derived corpus by natural language or identifiers and to retrieve publication details while traversing bounded citation and semantic literature graphs.

Enables LLM-powered applications to look up bacterial and archaeal taxonomy, search genomes, browse and navigate the taxonomic tree, and compare genomes or find phylogenetic paths between taxa. It works out of the box with a built-in reference dataset covering major phyla and can be pointed at full Genome Taxonomy Database TSV files for comprehensive queries.

Enables AI assistants to submit genomic sequences or NCBI accessions to antiSMASH for secondary metabolite biosynthetic gene cluster analysis, check job status, retrieve and download results, and query server status across bacteria, fungi, and plant servers.

Enables users to search rRNA sequences by organism, accession, or taxonomy, retrieve detailed sequence metadata, evaluate probes and primer pairs, and list available databases and taxonomies through MCP tools.

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

Enables searching ENA's public sequencing data by organism, study, platform, country or date, retrieving FASTQ/BAM download URLs and checksums, and discovering available result types and fields.

Enables AI agents to search EBI BioSamples metadata for biological samples such as cell lines, tissues, and organisms by free-text keyword, and to fetch individual records by accession to retrieve taxId, organism, and characteristics like tissue, sex, and cell type. It can run as a hosted gateway endpoint or locally over stdio via npx.

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 agents to search protein family, domain, and functional-site entries, read entry metadata and clan relationships, map a UniProt protein's annotations to residue coordinates, and find proteins carrying a given signature. Runs over STDIO or Streamable HTTP with no credentials required.

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 AI agents to resolve genes, diseases, chemicals, variants and species to normalized ids, search ~36M PubMed abstracts and PMC full texts by free text or entity, and retrieve the machine-extracted relations between them with the supporting sentences and PMIDs. Supports auditing individual relations with full evidence passages and pulling per-article entity annotations with character offsets.

Enables Claude, Cursor, or any MCP client to query public Drosophila connectome datasets and run in-silico experiments on them locally, with every answer carrying built-in controls, uncertainty, and provenance. Currently exposes dataset listing with licence, citation, download size, and locally cached level details.

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