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AutoGenes

AutoGenes generates worklists for the automation of the SpeedyGenes method for assembly of protein variant libraries:

SpeedyGenes: an improved gene synthesis method for the efficient production of error-corrected, synthetic protein libraries for directed evolution. Currin A, Swainston N, Day PJ, Kell DB. Protein Eng Des Sel. 2014, 27:273-80.

To run AutoGenes on Windows, open a Command Prompt, navigate to this directory and type:

run.bat

For Mac / Linux, open a Terminal window, navigate to this directory and type:

bash run.sh

Output will be generated in the out directory.

By default, these scripts will run AutoGenes according to the parameters in the run.bat or run.sh file.

The scripts run a Python command as follows:

python autogenes/run.py data/plates 2 3 out/ MAON

where:

  • data/plates specifies the directories in which the plate maps (as csv files) are located.

    • Two plate files are required, named wt.csv containing wildtype oligos, and mut.csv containing mutant oligos.
    • The existing files indicate the format and headings required.

  • 2 specifies the maximum number of mutants to consider per oligo;

  • 3 specifies the number of blocks to be assembled into a full length gene;

  • out specifies the directory to which to write output;

  • MAON is a short project name used to generate plate identifiers.