VirPrimer

Advanced viral primer design tool for molecular biology research

This website is free and open to all users.

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Online Computing

Efficient online computing platform that provides real-time primer design and analysis services. Based on the latest bioinformatics algorithms to ensure accuracy and reliability of results.

Launch Computing
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Download Software

Download the complete software package and related resources for offline use. Includes detailed user manual, sample data and technical documentation to meet your research needs.

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User Guide

Note: A brief operational workflow is provided below. For comprehensive instructions, please download and consult the Manual.

Loading Files

You can provide aligned or unaligned sequences:
  • Aligned inputs will be used directly for primer design
  • Unaligned inputs will be automatically aligned using MAFFT
Click the "+" button to add the required number of sequence groups. Click the "-" button to remove any unnecessary sequence groups.

Parameter Settings

Users can select parameters in the "Options" section according to specific experimental requirements. The "Options" module provides detailed parameter settings for primer design for each sequence set, including:
  • Melting temperature (Tm) range
  • Primer size specifications
  • GC content requirements
  • Product size range
  • Base proportion threshold
  • Thermodynamic formulas
Detailed information regarding parameter optimization can be found in the Manual, which is available for download.

Running VirPrimer

Click "Run" to execute the primer design process. The computation time will vary depending on the size and complexity of your input sequences.

Displaying and Saving Results

Once the computation is complete, click "Show Result" to display the output. The results interface presents designed primers with their corresponding properties and quality metrics. To save the generated results for subsequent analysis, click "Save Result."

Frequently Asked Questions

What input files are required?
The program accepts either aligned or unaligned FASTA files. If unaligned sequences are provided, VirPrimer will automatically perform multiple sequence alignment (MSA) using MAFFT.
Is it necessary to provide a reference genome or database to exclude off-target amplification?
When designing primers for sequence set A, sequences requiring exclusion of potential off-target effects should be merged into sequence set B and provided as the exclusion input. Alternatively, the data may be grouped into sets A and B, for which VirPrimer will design mutually non-interfering primers separately. Detailed information can be found in the Manual, which is available for download.
For multiplex PCR primer design, how many primer groups can VirPrimer handle simultaneously?
VirPrimer does not impose a strict limit on the number of primer groups. However, based on our experimental experience, we recommend designing up to five groups in practice, as this balance helps maintain primer uniformity, specificity, and sensitivity.
Why does this warning message occur?
The warning is triggered when at least one of your input sequence groups contains a proportion of valid bases below the predefined threshold. Users may either refine the input dataset by excluding such low-quality groups or, if desired, override the warning to proceed with primer design at their own discretion.
How do I cite VirPrimer?
Citation information will be available soon. Please check back for updates.

About VirPrimer

VirPrimer is a professional viral primer design tool dedicated to providing precise and efficient solutions for molecular biology research. Our platform combines advanced algorithms with comprehensive database resources to help researchers quickly design high-quality PCR primers. The tool is specifically optimized for viral genome analysis and supports both single and multiplex primer design workflows.