Team:Johns Hopkins-Software/theSoftware overview

From 2012.igem.org

(Difference between revisions)
Line 4: Line 4:
<div id="project_temp">
<div id="project_temp">
 +
 +
<div id="title">
 +
Software Goals
 +
</div>
-
+
<img src="https://static.igem.org/mediawiki/2012/a/af/SoftwareGoalsJHU.png"/>
<div id="title">
<div id="title">

Revision as of 00:53, 2 October 2012

Software Goals
AutoPlasmid


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.
Autogene

Retrieved from "http://2012.igem.org/Team:Johns_Hopkins-Software/theSoftware_overview"