Team:Davidson-MissouriW/Tools

From 2010.igem.org

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         <div id="Optimoose">
         <div id="Optimoose">
             <a href="http://gcat.davidson.edu/igem10/opt/opt_index.html">
             <a href="http://gcat.davidson.edu/igem10/opt/opt_index.html">
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                 <h3>The Optimoose</h3>
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                 <h3>Optimus</h3>
             </a><a NAME="optimoose">
             </a><a NAME="optimoose">
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                         </td>
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                         <td width=580>
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                             <p>The Optimoose is a tool designed to allow the user to evaluate the expression level of a gene sequence in <i>E. coli</i> using either RCBS-PC or the CAI formula.  Additionally, the user has the option to optimize or deoptimize the sequence by using one of those two formulas. If the optimized or deoptimized option is selected, the user will be given a new sequence whose codons have been changed to reflect the best, or worst, codons as determined by the selected formula. Assuming the entered sequence is in frame, the amino acid sequence is preserved.
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                             <p>Optimus is a tool designed to allow the user to evaluate the expression level of a gene sequence in <i>E. coli</i> using either RCBS-PC or the CAI formula.  Additionally, the user has the option to optimize or deoptimize the sequence by using one of those two formulas. If the optimized or deoptimized option is selected, the user will be given a new sequence whose codons have been changed to reflect the best, or worst, codons as determined by the selected formula. Assuming the entered sequence is in frame, the amino acid sequence is preserved.
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The Optimoose was designed to allow us to assign a given "weight" to the items, based on their protein production, to fill up the knapsack.</p>
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Optimus serves as a mechanism by which we can engineer optimized and deoptimized sequences which represent a given "weight" to the items in a knapsack based on their protein production.</p>
                         </td>
                         </td>
                         <td align=center width=600>
                         <td align=center width=600>

Revision as of 07:11, 29 July 2010

iGEM Davidson – Missouri Western 2010: Tools

The team has designed several tools in conjunction with our iGem project.













Construct Simulation

In order to better understand our fluorescent protein - TetA constructs, we designed a simulation of the cre-lox system. This simulation allows the user to test our pre-determined constructs as well as custom constructs from any number of promoters, lox sites, fluorescent proteins, essential genes, and/or terminators. The program will then show either a single, animated simulation that will allow the user to see how the lox sites interact, or it will run many simulations and then generate a histogram that shows the distribution of what fluorescent proteins were expressed. In addition, if the user chooses to include weights for the "items" and a capacity for the knapsack the program will tell you whether or not your construct has exceeded the capacity. In order to run the program, download the jar file. To see the actual percentages behind the histogram, the program needs to be run through a command line tool, but other than that simply double clicking the jar file to run it should be sufficient.

sim




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