Sequence concatenation and assembly: parameters and notes

See the tutorial for usage and examples.

Each function includes its purpose, API, inputs, outputs, example code and result description. Prepare any required credentials, local files and optional dependencies; remote results vary with database releases and query time.

Design overlaps for Gibson assembly

dnakit.databases.dna_gibson_design(*, operation=None, fragments, overlap_length=None, verbose=True)

Parameter	Type	Required / default	Description and constraints
operation	string	None	Operation (optional; defaults to 'gibson_design' for this tool).
fragments	array	Required	List of DNA fragment sequences (at least 2). Each must be longer than overlap_length. {"items": {"type": "string"}}
overlap_length	integer | null	None	Overlap length in bp for Gibson Assembly (default: 20 bp). Must be at least 1.
verbose	bool	True	Progress flag.

Determine Golden Gate reaction products

dnakit.databases.dna_golden_gate_assemble(*, operation=None, fragments, enzyme=None, circular=None, labels=None, verbose=True)

Parameter	Type	Required / default	Description and constraints
operation	string	None	Operation (optional; defaults to 'golden_gate_assemble' for this tool).
fragments	array	Required	The DNA sequences combined in the reaction (plasmids or linear parts), A/T/G/C only. At least 2. {"items": {"type": "string"}}
enzyme	string | null	None	Type IIS enzyme used in the reaction, e.g. 'BsaI' (default), 'BbsI', 'Esp3I'/'BsmBI', 'SapI'.
circular	boolean | null	None	Whether the inputs are circular plasmids (default true). Set false for linear parts.
labels	array | null	None	Optional names for the inputs (e.g. plasmid names), echoed in the assembly order. {"items": {"type": "string"}}
verbose	bool	True	Progress flag.

Design Golden Gate restriction sites and overhangs

dnakit.databases.dna_golden_gate_design(*, operation=None, parts, enzyme=None, verbose=True)

Parameter	Type	Required / default	Description and constraints
operation	string	None	Operation (optional; defaults to 'golden_gate_design' for this tool).
parts	array	Required	List of DNA part sequences to assemble (at least 2). A, T, G, C only. {"items": {"type": "string"}}
enzyme	string | null	None	Type IIS restriction enzyme to use. Options: 'BsaI' (default) or 'BbsI'.
verbose	bool	True	Progress flag.