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