Golden Hinges (full documentation here) is a Python library to find sets of overhangs (also called junctions, or protrusions) for multipart DNA assembly such as Golden Gate assembly.
Given a set of constraints (GC content bounds, differences between overhangs, mandatory and forbidden overhangs) Golden Hinges enables to find:
- Maximal sets of valid and inter-compatible overhangs.
- Sequence decompositions (i.e. position of cuts) which produce valid and inter-compatible overhangs, for type-2S DNA assembly.
- Sequence mutations (subject to constraints) which enable the sequence decomposition, in extreme cases where the original sequence does not allow for such decomposition.
PIP installation:
pip install goldenhingesWeb documentation:
https://edinburgh-genome-foundry.github.io/GoldenHinges/
Github Page (with examples)
https://github.com/Edinburgh-Genome-Foundry/GoldenHinges
Live demo:
http://cuba.genomefoundry.org/design_overhangs
License: MIT, Copyright Edinburgh Genome Foundry
Golden Hinges is part of the EGF Codons synthetic biology software suite for DNA design, manufacturing and validation.