MCP For Claude Marketplace
PCR Protocol Optimizer

PCR Protocol Optimizer MCP Connector for Claude

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Calculates optimal PCR parameters including annealing temperature, extension time, and reagent concentrations.

4 tools Official Updated Oct 1, 2026 Official Vinkius Partner
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This MCP server provides precise calculations for PCR (Polymerase Chain Reaction) optimization. It helps researchers determine critical reaction parameters such as annealing temperature using calculate_annealing_params, extension duration via calculate_extension_settings, required cycle counts with estimate_cycle_count, and specific molar concentrations through generate_reagent_concentrations. By accounting for template type, GC content, and polymerase characteristics, it ensures high-yield and specific DNA amplification.

pcrdnamolecular-biologygenomicslab-automation

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

calculate_annealing_params

Determines the optimal temperature for the primers to bind to the template

calculate_extension_settings

Calculates how long the extension phase should last based on the target size and enzyme speed

estimate_cycle_count

Predicts the number of thermal cycles required to reach detectable levels of the amplicon

generate_reagent_concentrations

Recommends the specific molar concentrations for the reaction mixture

See how to talk to your AI agent using PCR Protocol Optimizer.

What is the optimal annealing temperature for a primer with a Tm of 60°C and 50% GC content using genomic DNA?

The optimal annealing temperature is 55°C, and it is recommended to use a buffer additive to stabilize the reaction.

How long should the extension phase last for a 2000 bp amplicon using a High-Fidelity polymerase?

The extension time should be 2 minutes at the recommended temperature for High-Fidelity enzymes.

Recommend reagent concentrations for a 500 bp amplicon with 65% GC content using a Standard polymerase and plasmid DNA.

Recommended concentrations: dNTPs at 0.2mM, Magnesium at 1.5mM, Primers at 0.5uM, and an enhancer concentration of 5% to handle the high GC content.

The `calculate_annealing_params` tool calculates the temperature by evaluating the primer Tm, the GC content of the target, and the complexity of the template type.

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