Example gallery

Below are some examples that show the functionality of pydna in real-world scenarios.

• Example_Restriction: PCRing a gene out of the genome, and cloning into a vector using restriction and ligation.

• Example_Gibson: Gibson assembly of R. cellulolyticum genomic fragments into a plasmid, from the original Gibson assembly paper doi: 10.1038/nmeth.1318.

• Example_CRISPR: Using CRISPR with homologous recombination to delete genes by making two cuts in the genome, and repair it with an oligo. Used in the industrially relevant K. phaffi.

• Example_HT_cazyme_primer_design: Design primers for a high-throughput CAZyme library (uses the extra dependency teemi).

• Example_designing_primers_for_kozak_library: We explore the combinatorial space of the most abundant kozak sequences and make repair-primers for the experiments. We will use pydna to simulate and the CRIPSR experiment and the homology directed repair with the oligoes we make (uses the extra dependency teemi).