danymatute / overhang

Compendium of overhangs

EGF's Compendium of overhangs

This Python package generates a description of an input set of DNA overhangs and outputs a PDF file. Additionally, it evaluates suitability of an input set of overhangs for Golden Gate DNA assembly.

Install

pip install overhang

Usage

import overhang as oh

overhang = oh.Overhang("TCAT")
dir(overhang)

overhang_classes = oh.generate_all_overhangs()
oh.write_pdf_report(target="examples/compendium_Esp3I.pdf", overhangs=overhang_classes)

See compendium_Esp3I.pdf.

Inspect a set of overhangs for assembly:

overhangset = oh.OverhangSet(
    overhangs=["ATGG", "GAAA", "CACC", "GACT", "ATGG", "CCAG",], name="Example",
)
oh.write_overhangset_report("examples/set_report_Example.pdf", overhangset)
# Esp3I Tatapov plot (37 Celsius, 1 hour):

The first page of the report:

Improve an overhang set by removing the bad interactions:

overhangs = ['TAGG', 'ATGG', 'GACT', 'GGAC', 'TCCG', 'CCAG', 'CAGC', 'AGGC']
overhangset = oh.OverhangSet(overhangs=overhangs, name="Example 2")
overhangset.find_perfect_subset()
# Overhangs in subset: ['TAGG', 'CCAG', 'AGGC', 'TCCG']
# Number of overhangs in subset: 4
# Esp3I Tatapov plot (37 Celsius, 1 hour):

Another approach is to iteratively remove the worst weakly annealing, self-misannealing, and misannealing overhang interactions until the desired number of overhangs is reached.

Versioning

Overhang uses the semantic versioning scheme.

License = MIT

Overhang is free/libre and open-source software, which means the users have the freedom to run, study, change and distribute the software.

Overhang was written at the Edinburgh Genome Foundry by Peter Vegh.

Copyright 2021 Edinburgh Genome Foundry, University of Edinburgh