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Design and assembly of DNA molecules using multi-objective optimisation

View ORCID ProfileAngelo Gaeta, View ORCID ProfileValentin Zulkower, View ORCID ProfileGiovanni Stracquadanio
doi: https://doi.org/10.1101/761320
Angelo Gaeta
School of Biological Sciences, The University of Edinburgh, Edinburgh EH9 3BF, United Kingdom
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Valentin Zulkower
Edinburgh Genome Foundry, School of Biological sciences, The University of Edinburgh, Edinburgh EH9 3BF, United Kingdom
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Giovanni Stracquadanio
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  • For correspondence: giovanni.stracquadanio@ed.ac.uk
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Abstract

Rapid engineering of biological systems is currently hindered by limited integration of manufacturing constraints into the design process, ultimately limiting the yield of many synthetic biology workflows.

Here we tackle DNA engineering as a multi-objective optimization problem aiming at finding the best tradeoff between design requirements and manufacturing constraints. We developed a new open-source algorithm for DNA engineering, called Multi-Objective Optimisation algorithm for DNA Design and Assembly (MOODA), available as a Python package and web application at http://mooda.stracquadaniolab.org.

Experimental results show that our method provides near optimal constructs and scales linearly with design complexity, effectively paving the way to rational engineering of DNA molecules from genes to genomes.

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The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. All rights reserved. No reuse allowed without permission.
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Posted September 08, 2019.
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Design and assembly of DNA molecules using multi-objective optimisation
Angelo Gaeta, Valentin Zulkower, Giovanni Stracquadanio
bioRxiv 761320; doi: https://doi.org/10.1101/761320
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Design and assembly of DNA molecules using multi-objective optimisation
Angelo Gaeta, Valentin Zulkower, Giovanni Stracquadanio
bioRxiv 761320; doi: https://doi.org/10.1101/761320

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