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iGEM Davidson – MWSU 2010: Tools

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

The Oligator

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 final option is to add BioBrick ends to your sequence. This is helpful when cloning your sequence into a BioBrick plasmid. Simply choose which site you want to add to the 5' end. The options are a prefix digested with XbaI, a prefix digested with EcoRI or the entire prefix. You then choose which site you want to add to the 3' end. The options are a suffix digested with SpeI, a suffix digested with PstI or the entire suffix. However, if you choose to add a prefix, you must choose a suffix, and vice-versa. Furthermore, you also have the ability to add a custom prefix and suffix.


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.



Verifying BioBrick parts can be difficult and tedious by hand. To solve this problem, we have developed a tool to identify BioBrick parts and devices in a given DNA sequence. When a sequence is entered, the program checks the last archived version of the BioBrick Parts Registry. If your desired part is not found, you can attempt to align the sequence you entered with the part you desire. Since this search uses a real-time version of the registry, it can potentially find additional parts. When a device is found in your sequence, you can click to view the sequences of individual parts.


Knapsack Game

In order to aid in the understanding of the Knapsack Problem, we created a game. The game has two modes: tutorial and challenge, each of which asks the player to fill a knapsack of a certain capacity with given weighted items. The tutorial gives tips about the type of problem and only uses six weighted items. The challenge offers no help and asks the player to choose from nine weighted items.