GoldenGateAssembler

For the paper visit:

GGAssembler: precise and economical design and synthesis of combinatorial mutation libraries

Running the code

Create a cost sensitive degenerate codon sequence. You have two options:

1. Run in Colab
2. Use a local installation.

Run in colab

Follow the instructions in: colab oligo design

Local Instllation

Requirments

• python >= 3.7

Install

1. clone the repo: git clone https://github.com/Fleishman-Lab/dawdlib.git
2. Make sure the rust compiler is available with rustc --version

• In case it's not you try module load rust or install following: How to install Rust

3. Install using pip: pip install dawdlib/

Usage

Please follow the example notebook in (example/gg_oligo_design.ipynb if you're running locally).

General instructions

1. set the variable GG_temp in box 1.2 to 25 in order to follow the GGA reaction conditions in NEB's paper (ADD_REF)
2. set the following variables in box 1.2: a. W_PATH to be the working dir b. resfile_path to your input refile. Make sure that your file does not contain positions with a single option (they are treated as variable positions) c. dna_path to the sequence file. It should contain DNA seq of a parent design of your repertoire in fasta format. Do not forget to add lack of density before translating the protein back to DNA.

If you want to use three base pair gates instead of 4

1. Set the variable RESTRICTION_ENZYME in box 1.2 to have the restriction enzyme you wish to use (probably SapI)
2. Set the variable gatelength in box 1.2 to be 3
3. Change the PREFIX and SUFFIX variables to include restriction sites for your restriction enzyme. For SapI, this is GCTCTTC in PREFIX and GAAGACC in SUFFIX
4. Set the path to the ligation data in box 1.2.1. For SapI, you should be able to just keep my path or you can add a different one
5. Run box 1.2.1