Click on "Deploy Server".
Wait a few minutes for the server to deploy. Once ready, it will show a "Started" state.
In the chat, type @ followed by the MCP server name and your instructions, e.g., "@WetLab-MCP Design qPCR primers for my target sequence with Tm around 60°C."
That's it! The server will respond to your query, and you can continue using it as needed.
Here is a step-by-step guide with screenshots.
WetLab-MCP is a professional FastMCP server designed to bridge the gap between computational discovery and wet-lab execution. It provides a comprehensive suite of tools for qPCR primer design, cloning strategy optimization, and sequence specificity analysis, all integrated directly into your AI-assisted research workflow.
Starting with the industry-standard primer3-py engine, WetLab-MCP ensures deterministic, high-quality assay designs without ever needing an external API for core calculations.
Related MCP server: Patsnap-mcp
design_qpcr_primers: Local, deterministic qPCR primer design enforcing standard $T_m$ and GC% constraints.
design_cloning_primers: Intelligent cloning strategy with automatic restriction site detection and "junk" leader recommendations for high enzyme efficiency.
design_taqman_probe: Automated TaqMan internal oligo design with industry-standard quenching rules (no 5' G).
analyze_multiplex_compatibility: All-vs-all heterodimer analysis to detect cross-reactivity in multiplex PCR or panels.
design_multi_gene_panel: Greedy optimization for building non-conflicting primer sets for multiple targets.
check_primer_specificity: Live NCBI BLAST integration (blastn-short) to verify potential off-target binding.
WetLab-MCP can be added to Claude Desktop using one of the following methods.
uvx (Recommended)This is the fastest way to run WetLab-MCP without manual installation. Ensure you have uv installed.
Add this to your claude_desktop_config.json:
{
"mcpServers": {
"WetLab-MCP": {
"command": "uvx",
"args": ["wetlab-mcp"]
}
}
}pipIf you prefer a standard installation:
pip install wetlab-mcpThen add this to your claude_desktop_config.json:
{
"mcpServers": {
"WetLab-MCP": {
"command": "python",
"args": [
"-m",
"wetlab_mcp"
]
}
}
}Tool | Purpose | Key Inputs |
| qPCR assays | Sequence, Target $T_m$ |
| Cloning/Gibson | Overhangs, Target $T_m$ |
| Real-time PCR | Sequence, Primers, Probe $T_m$ |
| Off-target check | Primer Sequence (Internet req.) |
| Dimer analysis | List of Primers |
| Batch design | List of Genes ({name, seq}) |
Distributed under the MIT License. See LICENSE for more information.
Analyze a set of primers for potential cross-reactivity (heterodimers). Useful for multiplex PCR or panel design.
Args: primers: A list of primer sequences to analyze.
Returns: A JSON string with identified risk interactions and compatibility score.
Inputs: primers (required). Returns: result
Check if a primer sequence binds elsewhere in the genome using NCBI BLAST. Requires internet connection and may take 10-30 seconds.
Args: primer_sequence: The DNA sequence of the primer (15-30 bp).
Returns: A JSON string with specificity rating and top matches in nt database.
Inputs: primer_sequence (required). Returns: result
Design primers for cloning the entire sequence with optional 5' overhangs. Detects common restriction sites and suggests leaders for efficiency.
Args: sequence: Target DNA sequence (ORF/Fragment to amplify). fwd_overhang: Optional 5' overhang for forward primer (e.g., restriction site). rev_overhang: Optional 5' overhang for reverse primer. target_tm: Target melting temperature in °C (default: 60.0).
Returns: A JSON string with precise and suggested (leader-included) primer pairs.
Inputs: sequence (required), fwd_overhang, rev_overhang, target_tm. Returns: result
Design a set of non-conflicting primer pairs for multiple genes. Uses a greedy approach to minimize heterodimers between pairs.
Args: genes: A list of genes, each with 'name' and 'sequence' keys. target_tm: Target melting temperature for primers in °C (default: 60.0).
Returns: A JSON string with the selected non-conflicting panel and any failures.
Inputs: genes (required), target_tm. Returns: result
Design validated qPCR primer pairs for a given DNA sequence using Primer3.
Args: sequence: Target DNA sequence (ATCG only, min 100 bp). target_tm: Target melting temperature in °C (default: 60.0). product_size_range: Desired PCR product size range (e.g., '70-150'). num_pairs: Number of primer pairs to return (1-5, default: 3).
Returns: A JSON-formatted string with validated primer pairs or error information.
Inputs: sequence (required), target_tm, product_size_range, num_pairs. Returns: result
Design a TaqMan probe for the region between two primers. Ensures probe Tm is higher than primers and follows standard rules (no 5' G).
Args: sequence: Target DNA sequence containing the primer binding sites. primer_fwd: Forward primer sequence (5'->3'). primer_rev: Reverse primer sequence (5'->3'). target_probe_tm: Target melting temperature in °C (default: 68.0).
Returns: A JSON string with the designed probe or error message.
Inputs: sequence (required), primer_fwd (required), primer_rev (required), target_probe_tm. Returns: result
Recent tool additions, removals, and schema changes observed during successful MCP inspections.
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Scored across 6 tools
Each tool targets a distinct task in primer/probe design: specificity checking, multiplex analysis, cloning primer design, multi-gene panel design, qPCR primer design, and TaqMan probe design. There is no overlap in functionality.
All tool names follow a consistent verb_noun pattern (analyze_, check_, design_), making the tool purpose clear and predictable.
With 6 tools covering the core workflow of primer and probe design and validation, the number is well-suited to the server's purpose without being excessive or insufficient.
The tool set covers the full lifecycle of primer design: specificity checks, compatibility analysis, design for cloning, qPCR, multi-gene panels, and TaqMan probes. No obvious gaps are present for a primer design MCP.
Hosted DNA/RNA/protein tools: primers, oligos, PCR, cloning, CRISPR, alignment, batch & pipelines.
AI-powered bioprotocol optimization — generate, search, and manage lab protocols via MCP
Validated molecular biology tools: cloning, primers, CRISPR, Sanger, alignment, qPCR, phylogenetics
90 molecular biology tools: plasmid maps, digests, primers, CRISPR, cloning, PubMed, lab notebook.
