This repo is a collection of scripts that can be used together to automate ordering of enzyme designs via Kunkel mutagenesis on Transcriptic.

Put your designed PDBs into a folder and modify order.bash to look for designs in that folder. Also include a path to the wild type nucleotide sequence of the gene that was used to generate the ssDNA. Run

bash order.bash | transcriptic submit -p project_name

to submit the Kunkel run.

The script will execute a glob query to find all the designs in a folder and iterate over them. It will pull out the protein sequence from the PDB and align the protein sequence to the nucleotide sequence using blastx. Python helper scripts then diff the two sequences, generate the mutagenic oligos necessary to transform one sequence into another, format the oligos for ordering, and generate autoprotocol for use on Transcriptic's platform.

Questions, comments, and pull requests welcome as this is still very much a work in progress!