SCHEMA-library-design

Tools for designing site-directed recombination libraries using SCHEMA and RASPP

General Workflow:

1. Generate pickled multiple sequence alignment (MSA) and contacts files. The MSA file should be a 2D list where every element of the outer list contains the amino acids of all sequences at a specific position. The contacts file numbering must be indexed from 0 and correspond to the MSA positional numbering.
2. Use run_raspp.py with the pickled MSA and contacts files as input to generate SCHEMA_gg libraries.
3. Run read_raspp_GG_output.py to select a library and save it as a pickled file.
4. Use generate_gg_dna.py with the codon-aligned nucleotide sequences to generate golden gate fragments for ordering.