MCP For Claude Marketplace
Primer Design Calculator

Primer Design Calculator MCP Connector for Claude

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Design optimal PCR primers and analyze their thermal and structural properties.

4 tools Official Updated Oct 1, 2026 Official Vinkius Partner
More Details Connect to Claude

This MCP server provides a complete suite of tools for PCR primer design. It allows users to generate optimal primer pairs using design_primers, evaluate structural risks like hairpins and dimers with analyze_stability, calculate physical properties via calculate_thermodynamics, and ensure target accuracy with verify_specificity. It is designed to help researchers ensure high-quality amplification by managing Tm, GC content, and specificity.

pcrdnaprimersgenomicsbiotechnology

4 tools expose this connector's capabilities to your AI agent.

design_primers

Generates a pair of optimal primers based on a target DNA sequence and user-defined constraints

verify_specificity

Checks if the proposed primers will bind to unintended locations in a provided genomic reference

analyze_stability

Evaluates the risk of secondary structures like hairpins and dimers for a specific primer or pair

calculate_thermodynamics

Provides detailed physical properties for a specific DNA sequence

See how to talk to your AI agent using Primer Design Calculator.

Design primers for the sequence ATGCATGCATGC with an amplicon size of 20.

The designed primers are: Forward: ATGCATGC, Reverse: ATGCATGC. The amplicon size is 20 and the design is optimal.

What is the GC content of the sequence GGGCCCAAATTT

The GC content for the sequence GGGCCCAAATTT is 50%.

Check if the primer ATGCATGC is specific to the genome ATGCATGCGGGGAAAA

The primer is specific to the target sequence with no unintended binding sites found.

You can use the `design_primers` tool by providing the target DNA sequence and the desired amplicon size.

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