Team:Johns Hopkins-Software/theSoftware overview

We recognized a need for a comprehensive piece of software that provided the means to achieve an easier Plasmid Design process. Manual annotation is simply too time consuming, tedious, and error-prone. We wanted to create something to fix this noticeable setback of existing synthetic biology software. AutoGene sets a new technological standard by bringing automation to the plasmid design process. That being said, we developed a list of specific goals we wished to achieve. We split these goals into two modules, and decided the first set of goals would be achieved by AutoPlasmid, the second set of goals would be achieved by AutoDesign, and together, we would create AutoGene.

Each of these goals encompasses an extensive list of sub-goals. Here, we discuss the more detailed goals for our primary milestones listed above.

AutoPlasmid is a simple-to-use annotation tool. Hand it a sequence of DNA, however big or small you'd like. Import a file or copy and paste the sequence.



Then sit back and watch. AutoPlasmid will search through a database containing 40,000 features and look for matches. Not only does it find perfect matches, but if you specify, you can search for imperfect matches with any threshold you'd like (ex. 90% match).



After searching for annotations, open your plasmid to look inside.



Interact with it by selecting features, manipulating the DNA, and adding any custom annotations you'd like. You can even view amino acid translations or oligo matches.







Lastly, you can view the details of an imperfect match.



AutoPlasmid is also compatible with a variety of standard biology tools, such as Ape. A plasmid can be imported as a fasta, gb, and SBOL file, as well as being exported as a fasta, gb, or SBOL file.

AutoDesign

AutoDesign takes the automation process to the next level. Using the annotated features that AutoPlasmid finds, the user may select features to design a new plasmid with. First, the user chooses features and drags them into the private registry.



Next, the user drags features into the private registry. The user can change the order of features, invert features, duplicate features, and delete features. At the same time, the user sees an updated version of the plasmid they are designing and the associated DNA.