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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 multi-method assemblies

Submit an assembly plan and parts records, get the final construct sequences or an analysis of design flaws. To try an example, select the example file for each upload box, and submit the form. If you want to simulate Golden Gate assemblies in particular, try this other app.

Provide an assembly plan

Only the connector parts necessary to obtain assemblies will be selected and added to the other parts.

Examples

multi_assembly.xlsx

 

An assembly plan with many different cloning methods used (Golden Gate, Gibson, BioBrick, LCR and Basic assembly).

Drop a file here or click to upload

Part names in the picklist refer to

• The IDs of the provided records
• The file names (without extension)

Provide parts to assemble

Upload all the parts sequences for your assemblies. Don't forget the receptor vectors.

Examples

part_sequences.zip

 

Genbank and fasta records of all parts needed in the assembly plan

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)

Autoselect connectors

• 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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