Gibson Assembly
AI Scientist provides a complete Gibson isothermal assembly workflow through the /gibson command. The entire process — from fragment collection to assembly simulation — is handled within a single conversation, producing ready-to-order primers and annotated construct files.
Assembly Workflow
Section titled “Assembly Workflow”The Gibson assembly pipeline follows six sequential steps:
| Step | Action | Details |
|---|---|---|
| 1 | Sequence Collection | Automatically retrieve fragments from your sequence library or NCBI |
| 2 | Vector Linearization | PCR inverse amplification (recommended) or restriction enzyme digestion |
| 3 | Overlap Design | 25-40bp overlap regions are automatically calculated between adjacent fragments |
| 4 | Assembly Primer Design | Generate overlap-containing primers for each fragment |
| 5 | Assembly Simulation | Simulate multi-fragment Gibson assembly and generate the complete circularized product |
| 6 | Annotation & Delivery | Auto-add feature annotations, export GenBank files, and save to your sequence library |
Multi-Fragment Support
Section titled “Multi-Fragment Support”AI Scientist supports 2-6 fragment assemblies in a single operation. The system automatically handles:
- Direction correction — detects and corrects fragment orientation to ensure proper assembly order
- Overlap optimization — adjusts overlap lengths to balance Tm uniformity across all junctions
- Conflict detection — identifies potential issues such as repeated sequences at junctions or incompatible overlaps
Output
Section titled “Output”After simulation, you receive:
- A complete annotated GenBank file of the assembled construct
- A primer ordering table (CSV/TSV) for all assembly primers
- An interactive sequence map showing all fragments, overlaps, and features
- The assembled construct saved to your component memory library for future use