Pydna

Welcome to pydna’s documentation!

Pydna is a python package that provides a human-readable formal descriptions of 🧬 cloning and genetic assembly strategies in Python 🐍 for simulation and verification. Pydna can be used as executable documentation for cloning.

Designing genetic constructs with many components and steps, like recombinant metabolic pathways 🧫, often makes accurate documentation difficult, as seen in the poor state of scientific literature ☢️

A cloning strategy expressed in pydna is complete, unambiguous and stable.

Pydna provides simulation of:

• Primer design

• PCR

• Restriction digestion

• Ligation

• Gel electrophoresis of DNA with generation of gel images

• Homologous recombination

• Gibson assembly

• Golden gate assembly (in progress)

Virtually any sub-cloning experiment can be described in pydna, and its execution yield the sequences of intermediate and final DNA molecules.

Pydna has been designed with the goal of being understandable for biologists with only some basic understanding of Python.

Pydna can formalize planning and sharing of cloning strategies and is especially useful for complex or combinatorial DNA molecule constructions.