set_seq_strand

You can download the script here.

Used for changing sequences of whole strands in an origami and prints out the new topology file.

Remember: oxDNA sequences run 3’-5’ (opposite to the usual way of 5’-3’)!

Usage:

python set_seq_strand.py conf_file top_file virt2nuc seq_file

Args:

• conf_file: configuration file
• top_file: topology file
• virt2nuc: virt2nuc file (can be generated from cadnano_interface.py with a cadnano json file)
• seq_file: file containing strand sequences (details described below)

Notes:

An example seq_file is shown below:

0 16 stap AAAAAAAAAAAAAAAA

This will change the sequence for the strand containing the specified nucleotide at (vh, vb, type) to AAAAAAAAAAAAAAAA. vh and vb stands for virtual base index and virtual helix index in cadnano, and type is either stap (staple) or scaf (scaffold).