Design-A-Genome with GeneDesign and BioStudio
Sarah Richardson, Johns Hopkins University School of Medicine
GeneDesign is a nucleotide manipulation pipeline for the design of synthetic genes. We host a public and freely accessible server at genedesign.org, and the source is available from GitHub for download under the New BSD License. Since GeneDesign was published and made publicly available 3 years ago, we have made its code base more efficient, added new algorithms and modules, updated the restriction enzyme library, and most importantly, added batch processing capabilities and several command line modules. The latter easily lend GeneDesign to integration with other synthetic design platforms.
BioStudio is a framework for the multi-scale design of synthetic genomes. It can modify nucleotide sequences automatically or manually at multiple resolutions, using the GeneDesign libraries where appropriate. It uses the excellent open-source and user-friendly GBrowse as a GUI. It is currently able to locate and manipulate potential and existing restriction enzyme recognition sites, select recognition sites for the physical assembly of designed sequence, identify and incorporate unique sequences for PCR identification of wildtype and synthetic sequence, edit existing genome features, and create and annotate user-created genome features. BioStudio annotates all changes to the genome sequence for version control, allowing the “roll-back” of any modifications with lethal phenotypes. When coupled with a modular design strategy, versioning allows genome synthesis to proceed with as little re-synthesis as possible. In addition, BioStudio includes a detailed database schema that can serve as a synthesis tracking and workflow management tool. BioStudio is currently in use by the synthetic Saccharomyces Cerevisiae project and will be available as a public server and for download as an open source package by the end of the year.