Team:Davidson-MissouriW/Tools

From 2010.igem.org

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                             <p>Designing and building DNA sequences is a fundamental tool for anyone who works in synthetic biology.  The Oligator is designed to choose oligos to create any desired sequence between 20 and 20,000 base pairs.  The program allows the user to choose oligo lengths between 20 and 160 bp and overlap lengths of between 20 and 80 bp.   
                             <p>Designing and building DNA sequences is a fundamental tool for anyone who works in synthetic biology.  The Oligator is designed to choose oligos to create any desired sequence between 20 and 20,000 base pairs.  The program allows the user to choose oligo lengths between 20 and 160 bp and overlap lengths of between 20 and 80 bp.   
The program will also check for and remove BioBrick restriction sites at the request of the user. Choosing the first checkbox will tell the user if BioBrick restriction sites exist anywhere in the entered DNA sequence and embolden where they occur. The second checkbox will remove the sites, leaving the amino acid sequence intact. Since keeping the amino acid sequence the same involves knowing the reading frame, a radio button must be filled in indicating where the reading frame begins.
The program will also check for and remove BioBrick restriction sites at the request of the user. Choosing the first checkbox will tell the user if BioBrick restriction sites exist anywhere in the entered DNA sequence and embolden where they occur. The second checkbox will remove the sites, leaving the amino acid sequence intact. Since keeping the amino acid sequence the same involves knowing the reading frame, a radio button must be filled in indicating where the reading frame begins.

Revision as of 21:38, 27 July 2010

iGEM Davidson – Missouri Western 2010: Tools

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





Construct Simulation

In order to be able to better understand how to build our constructs to give us the best system for solving the knapsack problem we created a simulation of the cre-lox system. This simulation allows the user to test several pre-determined constructs that out team came up with. In addition, one can create their own custom construct 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 create 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