oogga 0.0.0

Overhang Optimizer for Golden Gate Assembly

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

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Installation

pip install oogga

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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.

1. Download the zip from:
   https://pubs.acs.org/doi/suppl/10.1021/acssynbio.8b00333/suppl_file/sb8b00333_si_002.zip

2. Extract it and open FileS04_T4_18h_37C.xlsx in Microsoft Excel or LibreOffice Calc.

3. Save as FileS04_T4_18h_37C.csv (in CSV format).

4. Pass the path to this CSV file with the -data_file argument or copy to ./lib/.

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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

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Evaluate overhangs (eval-frags)

This script is used in the manuscript

eval-frags AACC TTGG ACGT TGCA