Team:Davidson-MissouriW/Tools
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<div id="mission_box"> <h2> iGEM Davidson – Missouri Western 2010: Tools </h2> | <div id="mission_box"> <h2> iGEM Davidson – Missouri Western 2010: Tools </h2> | ||
- | <h3>The team has designed several tools | + | <h3>The team has designed several tools to guide and support our iGEM project.</h3> |
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- | <p>Verifying BioBrick parts can be difficult and tedious by hand. To solve this problem, we have developed a tool to identify BioBrick parts | + | <p>Verifying BioBrick parts can be difficult and tedious by hand. To solve this problem, we have developed a tool to identify BioBrick parts within a given DNA sequence. When a sequence is entered, the program checks the last archived version of the BioBrick Parts Registry and returns the best matched part. If your desired part is not found, you can attempt to align the sequence you entered with the part you desire. When a device is found in your sequence, you can click to view the sequences of individual parts. An alignment of the sequence with the part is presented to the user allowing for easier sequence analysis.</p> |
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<a href="http://gcat.davidson.edu/igem10/opt/opt_index.html"> | <a href="http://gcat.davidson.edu/igem10/opt/opt_index.html"> | ||
- | <h3> | + | <h3>Optimus</h3> |
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- | <p> | + | <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. |
- | + | 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> | |
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- | <a href="http://gcat.davidson.edu/igem10/opt/opt_index.html"><img src="https://static.igem.org/mediawiki/2010/ | + | <a href="http://gcat.davidson.edu/igem10/opt/opt_index.html"><img src="https://static.igem.org/mediawiki/2010/2/25/Davidson-MissouriWoptimus.png" alt="Tools" width=280/></a> |
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<a NAME="Simulator"> | <a NAME="Simulator"> | ||
<a href="https://static.igem.org/mediawiki/2010/4/4a/ConstructSim.zip"> | <a href="https://static.igem.org/mediawiki/2010/4/4a/ConstructSim.zip"> | ||
- | <h3> | + | <h3>SimuLox</h3> |
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- | <a href="https://static.igem.org/mediawiki/2010/4/4a/ConstructSim.zip"><img src="https://static.igem.org/mediawiki/2010/ | + | <a href="https://static.igem.org/mediawiki/2010/4/4a/ConstructSim.zip"><img src="https://static.igem.org/mediawiki/2010/8/87/Davidson-MissouriWconsim.png" alt="sim" width=355/></a> |
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Latest revision as of 22:19, 22 October 2010
iGEM Davidson – Missouri Western 2010: Tools
The team has designed several tools to guide and support our iGEM project.
VeriPart
The Oligator
Optimus
SimuLox
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. |
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