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• Scenarios
  Sculpt a Sequence
  Design Golden Gate Overhangs
  Simulate Golden Gate
  Simulate multi-method assemblies
  Insert Parts on Backbones
  Sketch Constructs
  Convert Sequence Files
  Domesticate Part Batches
  Transfer Genbank Features
  Substitute Parts Overhangs
  Design Sites Arrays
  Plot Sequence Features
  Evaluate Manufacturability
  Find Common DNA Blocks
  Compare Two Sequences
  Render Sequenticons
  View Overhangs Crosstalk
  Predict Bad Clone Rates
  Extract Features
  Predict Digestions
  Select digestions
  Analyze Digests
  Select primers
  Find Saboteur Parts
  Design Part Test Batches
  Create Assembly Picklists

Simulate Golden Gate Assemblies

Submit parts and an assembly plan. Get annotated Genbanks of the resulting construct(s), or an analysis of design flaws.

Provide parts to assemble

Upload all the parts sequences for your assembli(es). Don't forget the receptor vector(s).

Examples

example_genetic_parts_and_backbone.zip

 

Genbank records of five parts (A, A2, B, B2, C) and receptor vector. the parts can go into one of 3 possible slots, forming a total of four possible assemblies.

2-step_golden_gate_parts.zip

 

Parts for a 2-step golden gate assembly (if you choose this example, also select the example 2-step assembly plan to go with it).

parts_for_sapI_assembly.zip

 

SapI-based single assembly

parts_missing_connectors.zip

 

Genbank records of 11 parts which could form a circular assembly if they were completed with connectors. Tick "autoselect connectors" below and load the "example connectors", then press "Predict final constructs".

Drop a file here or click to upload

Accepted formats: FASTA, Genbank, Snapgene

• All sequences are circular
• All sequences are linear
• Autodetect each sequence's topology (default to circular)
• Autodetect each sequence's topology (default to linear)

Restriction enzyme

• BsaI
• BsmBI
• BbsI
• SapI
• AarI
• Autoselect from part sequences

Other options

Autoselect connectors

Provide a list of assemblies

Use file names as part IDs

Force the backbone to be in first position

Include constructs plots

• Plot parts and fragments on assembly failure only
• Plot parts and fragments (slower)
• Don't plot parts and fragments

• Plot graphs on assembly failure only
• Always plot graph (slower)
• Don't plot graph

Predict final construct(s)

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