pydna.gateway

Assembly of sequences by Gateway recombination.

Given a list of sequences (Dseqrecords), all sequences are analyzed for presence of att(P|B|L|R)N where N is 1,2,3 or 4.

A graph is constructed where the att sites form a nodes and sequences separating att sites form edges.

The NetworkX package is used to trace linear and circular paths through the graph.

class pydna.gateway.Gateway(molecules=None)

Bases: object

Assembly of linear DNA fragments into linear or circular constructs.

The Assembly is meant to replace the Assembly method as it is easier to use. Accepts a list of Dseqrecords (source fragments) to initiate an Assembly object. Several methods are available for analysis of overlapping sequences, graph construction and assembly.

Parameters:

fragments (list) – a list of Dseqrecord objects.