Comments (2)
Hey! Gibson assembly from parts is possible but not straightforward. I'm not sure what doesn't work for you, but here are some tricks:
- The simplest way to implement Gibson Assembly is using a
PcrExtractionStation
rather than aPartsLibrary
. The PCR station is more powerful. It will design primers to PCR your parts and so can either use a whole part, or a fragment of a part (by using primers that anneal inside the part), or a part with some added nucleotides on the flank (by adding these nucleotides to the ends of the primers). - Part libraries can work too but have an all-or-nothing way of providing parts, they need to be asked for an exact DNA fragment that's in the collection. If your PCRed parts in your collection already include overlaps between parts, and these overlaps were computed in a way that's not exactly the one using by the GibsonAssemblyStation, it probably won't work.
- Whether you are using a PCR station or a Library part, don't forget to run
prepare_network_on_sequence(sequence)
before you compute the quote. This will recognize your part in the sequence to build, accelerate the computations and increase your chances of success:
... create your network
main_station.prepare_network_on_sequence(sequence)
quote = main_station.get_quote(sequence)
There's an example of Gibson assembly from parts in the SynBioCad project. Here's the problem description, here is how it defines the network and here is how it uses it. It may be less minimal than what you are after, it does a few extra things like reusing previously-built primers, handling circular sequences, having a Golden Gate alternative, etc.
Does that help?
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Thanks for the swift response @Zulko, this is a big help!
I had not discovered the SynBioCad repo. This looks very similiar to what I want to achieve, so I will try to start from there and modify it slightly.
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Related Issues (12)
- dealing with circular DNA HOT 18
- File Not Found Error during assembly_report execution HOT 2
- What to do when Gibson assembly Station is refused : Apologies to put a routine use question as an issue HOT 10
- Contact Zulko HOT 7
- verify_constraints performance HOT 3
- SBOL => Automation MoClo Assembly tool => Optimal assembly report HOT 2
- Does the PartsLibrary work for circular sequences? HOT 3
- What role cut_spread_radius plays in circular sequence decomposition? HOT 1
- Q: Any specific reason why PcrExtractionStation not using the PartsLibrary? HOT 1
- Bug: Max length initialisation HOT 2
- Bug: When quote.assembly_plan is None
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