schemarecomb.breakpoints.BreakPoint

class schemarecomb.breakpoints.BreakPoint(position: int, overhangs: list)

Valid site for Golden Gate Assembly in a parent alignment.

A BreakPoint is where an alignment may be cut and recombined to form chimeric sequences. Also known as “crossover” or “recombination site”.

Parameters

position –

Index within a ParentSequence.alignment where the BreakPoint

is located. Note carefully that this attribute denotes where a new chimeric block begins. The last amino acid of the previous block is located at position-1. The Golden Gate sticky ends will overlap the codons of amino acids position-1 and position.

overhangs: Valid Golden Gate overhangs, containing the overhang DNA

start site relative to the codon at position-1 and the overhang string. 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…”.