Revision as of 15:55, 27 July 2010 by Stmeador (Talk | contribs)

iGEM Davidson – MWSU 2010: Tools

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


The Optimoose

The Optimoose is a tool designed to allow the user to evaluate the expression level of a sequence from ecoli using either RCBS-PC or the CAI formula. The RCBS-PC, or Relative Codon Bias value takes the observed codon frequency and substract it to the expected codon frequency and divides by the expected frequency. The CAI, or Codon Adaptation Index takes the frequency of each codon in a host organism and divides it by the frequency of each codon that appears the most in the host organism; and raise that result to the 1 over L power. The user has then the option to either optimized or deoptimized the sequence by using one of those two formulas. If the optimize or deoptimize option is selected the user will be given a new sequence in which the codons have been changed to reflect the best, or worst, codons as determined by the selected formula. However, the amino acid sequence is preserved. The Optimoose was designed to allow us to assign a given weight to the items to fill up the knapsack. Based on how optimized or deoptimized the sequence is , and based on the capacity of the knapsack; we could give every items a weight to satisfy our goals.


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.