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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):

Plot

The first page of the report:

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):

Plot 2

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.