Biodevisor: Automated Refactoring of Biosynthetic Gene Clusters

The Build-OptimizatiOn Software Tools (BOOST) (https://boost.jgi.doe.gov) automate the design of DNA sequences, ready for a minimal cost- and time-efficient manufacturing process with a maximum success rate. Current BOOST functionalities include: (i) reverse-translation of protein sequences into DNA sequences, (ii) codon juggling of protein coding DNA sequences ("CDS"), (iii) verification of DNA sequences against synthesis criteria (e.g., %GC content, repeats), (iv) modification of DNA sequences in case of violations, and (v) partitioning of large DNA sequences into synthesizable building blocks.

Here, we demonstrate BioDevisor, a newly developed contribution to BOOST to automate the workflow of refactoring biosynthetic gene clusters. At minimum, the user inputs (i) the sequences of the cluster's genes, (ii) information about the target host, and (iii) the synthesis criteria. Then, BioDevisor outputs the synthesizable DNA sequences of the gene cluster. Throughout the automated workflow, BioDevisor considers synthesis criteria by integrating existing BOOST functionalities. In addition, BioDevisor builds upon existing software tools and data repositories, such as RBS Calculator (https://salislab.net/software/), Eugene (http://www.eugenecad.org), ICE (https://public-registry.jbei.org/), SynBioHub (http://synbiohub.org/).