siRNA design tool

Design effective siRNA sequences with target specificity scoring and off-target prediction

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About This Tool

This siRNA design tool helps researchers create effective small interfering RNA (siRNA) sequences for gene silencing experiments. The tool analyzes your target mRNA sequence, generates multiple siRNA candidates, and evaluates them based on established design rules including GC content, thermodynamic properties, and target specificity. It also provides off-target prediction to minimize unintended gene silencing. The tool supports multiple species and allows customization of design parameters for optimal results.

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How to Use

Enter your target mRNA sequence in FASTA format or plain text
Select the target species from the dropdown menu
Adjust design parameters if needed (GC content range, siRNA length)
Click 'Design siRNA' to generate candidate sequences
Review the results table showing sequence, GC content, specificity score, and off-target prediction
Select your preferred siRNA sequence for further analysis

Frequently Asked Questions

Find Quick Answers

What is siRNA and why is proper design important?

siRNA (small interfering RNA) is used in RNA interference to silence specific genes. Proper design is crucial for effectiveness and minimizing off-target effects that could silence unintended genes.

What design rules does this tool follow?

The tool follows established siRNA design rules including optimal GC content (30-55%), avoidance of internal repeats, thermodynamic stability considerations, and target site accessibility prediction.

How accurate is the off-target prediction?

The off-target prediction uses sequence homology matching against the selected species' transcriptome database to identify potential unintended targets with high sequence similarity.

Can I use this tool for any species?

The tool currently supports human, mouse, rat, zebrafish, and drosophila species with pre-loaded transcriptome databases for accurate off-target prediction.

What format should I use for the target sequence?

You can paste sequences in FASTA format (starting with '>') or plain nucleotide sequences (A, T, C, G, U). The tool automatically detects and processes both formats.

Need to run multiple calculations?

Create a free account today to unlock unlimited daily runs, access advanced parameters, save your history, and request custom features.

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