schemarecomb.restriction_enzymes.RestrictionEnzyme

class schemarecomb.restriction_enzymes.RestrictionEnzyme(name, recognition_seq, top_cut_dist, bottom_cut_dist, ligation_counts)

Type IIS restriction enzyme used in Golden Gate Assembly reaction.

Only restriction enzymes that create three or four base overhangs are currently supported.

Parameters

• name (str) – Name of the restriction enzyme.

• recognition_seq (str) – Sequence of DNA bases recognized by enzyme. By convention, the cut site must be downstream of this sequence.

• top_cut_dist (int) – Distance from the end of recognition_seq where the top strand (containing the recognition_seq) is cut.

• bottom_cut_dist (int) – Distance from the end of recognition_seq where the bottom (complementary) strand is cut.

• ligation_probs – For each pair of possible DNA overhangs, the relative count of ligating together. Generally comes from the read_ligation_data function.

Attributes

• name – Name of the restriction enzyme.

• recognition_seq (str) – Sequence of DNA bases recognized by enzyme. By convention, the cut site must be downstream of this sequence.

• top_cut_dist (int) – Distance from the end of recognition_seq where the top strand (containing the recognition_seq) is cut.

• bottom_cut_dist (int) – Distance from the end of recognition_seq where the bottom (complementary) strand is cut.

• overhang_len (int) – Length of the overhang (sticky end) sequence.

• ligation_counts – For each pair of possible DNA overhangs, the relative count of ligating together.

Raises

ValueError – If the input overhang length is not 3 or 4, or if the keys of ligation_counts does not contain all possible overhangs of the correct length.