Overhang Optimizer for Golden Gate Assembly
Project description
Overhang Optimizer for Golden Gate Assembly (OOGGA)
Python package for fragmenting DNA sequences optimally for Golden Gate assembly cloning.
How the OOGGA works and OOGGA citation:
Overhang Optimizer for Golden Gate Assembly (OOGGA) S. Mukundan, M. S. Madhusudhan bioRxiv 2025.06.16.659877; doi: https://doi.org/10.1101/2025.06.16.659877
Installation
pip install oogga
Getting the overhang scores
OOGGA requires a CSV scoring table from Potapov et al. 2018. Please use the data from the journal website and cite them.
Potapov V, Ong JL, Kucera RB, Langhorst BW, Bilotti K, Pryor JM, Cantor EJ, Canton B, Knight TF, Evans TC Jr, Lohman GJS. Comprehensive Profiling of Four Base Overhang Ligation Fidelity by T4 DNA Ligase and Application to DNA Assembly. ACS Synth Biol. 2018 Nov 16;7(11):2665-2674. doi: 10.1021/acssynbio.8b00333. Epub 2018 Oct 29. PMID: 30335370.
-
Download the zip from:
https://pubs.acs.org/doi/suppl/10.1021/acssynbio.8b00333/suppl_file/sb8b00333_si_002.zip -
Extract it and open
FileS04_T4_18h_37C.xlsxin Microsoft Excel or LibreOffice Calc. -
Save as
FileS04_T4_18h_37C.csv(in CSV format). -
Pass the path to this CSV file with the
-data_fileargument or copy to ./lib/.
Usage
See all command line options
oogga -h
A normal example of splitting a plasmid into fragments of length range 500-1000
oogga inputplasmid.fasta 500 1500 output
Evaluate overhangs (eval-frags)
This script is used in the manuscript
eval-frags AACC TTGG ACGT TGCA
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