schemarecomb.breakpoints.Overhang

class schemarecomb.breakpoints.Overhang(ind: int, seq: str)

Valid Golden Gate Assembly overhangs (sticky ends).

Parameters

• ind – Index of the start site relative to the codon at one less than the breakpoint’s position - 1. For example, the (1, ‘TGTG’) overhang would be a sticky end that is one base pair right of the codon at position-1. So if the alignment only has ‘M’ and ‘W’ at position-1 and position, respectively, “ATG” and “TGG” are the only codons that may appear at these indices. Then, with the overhang as upper-case, the assembled DNA sequence will be “…aTGTGg…”. An ind of -1 implies that the overhang is a dummy.

• seq – Sequence of the sticky end.