Welcome to protoSpaceJAM’s documentation!

protoSpaceJAM is a CRISPR knock-in design tool to design guide RNAs and DNA donors that maximizes success rate using an array of known rules.

Workflow overview

Check out the Usage section and our paper for more information. Source code is available.

Contents

• Usage
  • Basic usage
  • 1. Create a submission list
  • (Optional) Load an example submission list
  • 2. Verify the submission list
  • 3. Execute protoSpaceJAM
  • 4. View and download results
• Algorithm and parameters
  • Key concepts
  • Tunable parameters
  • gRNA scoring
  • Recoding strategy
  • DNA donor processing strategy
• Source code
• Changelog
  • Algorithm
  • Portal