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Edinburgh-Genome-Foundry / DnaCauldron

:alembic: Simple cloning simulator (Golden Gate etc.) for single and combinatorial assemblies
https://edinburgh-genome-foundry.github.io/DnaCauldron/
MIT License
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Check parts assembling into enzyme sites #10

Closed veghp closed 2 years ago

veghp commented 2 years ago

In this hypothetical scenario, the ends of two parts assemble into an enzyme site. If the overhang is in the middle 4 basepairs, the enzyme site will not be detected in the individual parts:

enzyme_site = "CGTCTC"
overhang = "GTCT"
part1 = "NNNNN" + "CGTCT"
part2 = "GTCTC" + "NNNNN"

Admittedly, this is an extreme edge case, but may be useful to implement a check on the final construct, possibly using biopython.Restriction. Example of final construct containing an enzyme site: assembly_simulation.zip