Team:Johns Hopkins-Software

AutoGene is an all-encompassing plasmid design suite meant to streamline the process of both annotating and building sequences. Consisting of two modules — AutoPlasmid and AutoDesign — it first uses a highly curated database of features to search an imported plasmid, scanning the sequence for both perfect and imperfect alignments, and generates an interactive visualization of the annotated plasmid. Once a plasmid is annotated, a user is then able to alter its contents, using the AutoGene feature database, the biobrick database, as well as custom components. The design module enables structural optimization by maintaining sets of sequence rules and taking an algorithmic approach to minimizing structural violations. Additionally the program reduces the problems caused by restriction sites during application of designs, and proposes the most suitable enzyme selections through an analysis of standard restriction sites libraries.

The process will be run on the cloud as a standard web server gateway interface service to dramatically increasing its speed and accessibility while maintaining the same level of accuracy. As a cloud service, it will run its algorithms in parallel and thus have the ability to perform more computationally intense procedures, such as optimizing codons to increase gene expression, and designing the most efficient oligonucleotide sequences for PCR assembly.

Furthermore, AutoGene has the potential for integrating fabrication or design software in the future. 3D visualization techniques could provide users with views of protein structures created from the sequences or that of a related ortholog. A process for fabrication of synthetic DNA sequences could be automated through a building block design and benefit the user in assembling the oligonucleotides together. A number of additional features such as evaluating overlapping segments of oligonucleotides and melting temperatures for PCR assembly may also be built on top of this project.

Using a clear user interface, a large, highly curated feature database, and a novel approach through cloud computing, we hope to simplify the process of plasmid design. AutoGene aims on making it faster and easier for a user to both identify and modify the contents of any plasmid, and enhancing sequences for greater viability and expression.