SecureDNA Scanner

Screen sequences for biosecurity concerns using the SecureDNA service.

What is SecureDNA?

SecureDNA is a biosecurity screening system that:

• Checks sequences against hazard databases

• Identifies potentially dangerous sequences

• Supports responsible genetic engineering

• Required by many synthesis providers

Running a Screen

From Tools

1. Click Tools in the sidebar

2. Select SecureDNA Scanner

3. Enter or paste sequence

4. Click Screen

From Construct Editor

1. Open a construct

2. Click the SecureDNA icon in the toolbar

3. Screen runs automatically on the full construct

Batch Screening

Screen multiple constructs:

1. Select constructs in repository

2. Right-click > Screen with SecureDNA

3. View results for all

Understanding Results

Clear Result

Your sequence passed screening:

• No hazardous sequences detected

• Safe to proceed with synthesis

• Keep results for records

Flagged Result

Potential concern detected:

• Review the flagged region

• Understand why it was flagged

• May need modification or justification

Result Categories

Category	Meaning
Pass	No concerns
Flag	Requires review
Block	Cannot proceed

Working with Flagged Sequences

Review Details

1. Click on flagged result

2. See specific concern

3. View flagged sequence region

Common Causes

• Toxin-encoding sequences

• Pathogen genes

• Virulence factors

• Dual-use research concern genes

Resolution Options

1. Modify sequence: Remove or alter problematic region

2. Provide justification: Document legitimate research purpose

3. Contact support: Get guidance on compliance

Synthesis Provider Requirements

Pre-Order Screening

Many providers require SecureDNA screening:

1. Screen your construct

2. Download screening certificate

3. Include with synthesis order

Export Certificate

1. View screening result

2. Click Download Certificate

3. PDF includes:

   • Sequence identifier

   • Screening date

   • Result summary

   • SecureDNA verification

Best Practices

Regular Screening

• Screen all constructs before synthesis

• Re-screen after modifications

• Keep screening records

Design Considerations

• Be aware of hazardous sequences

• Consider alternatives for flagged regions

• Document research justification

Compliance

• Follow institutional biosafety guidelines

• Maintain screening documentation

• Report concerns appropriately

Integration

Automatic Screening

Enable automatic screening:

1. Go to workspace settings

2. Enable SecureDNA on construct creation

3. All new constructs screened automatically

API Access

Screen programmatically via API for:

• Batch processing

• Pipeline integration

• Automated workflows

Troubleshooting

Screening Fails

• Check sequence validity

• Verify internet connection

• Try again later

Unexpected Flag

• Review the specific concern

• Check for sequence accuracy

• Contact support if unclear

Resources

• SecureDNA website

• Institutional Biosafety Committee

• Kernel support for screening questions

Next Steps

• BLAST Search — Sequence similarity

• Export Options — Export with certificates

• Creating Constructs — Design safe constructs