Davidson Missouri W/FalsePositiveProgram

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Latest revision as of 16:04, 9 July 2007

False Positives

The false positive programs will tell how many false positives there are in Adelman’s graph without two edges (12) and the other is for the original graph with 14 edges. To develop the program we first made a list of all the different ways to make each number represented in the path and numbered them. We also, numbered each of the edges. we took the numbered edges and made vectors of the ways that each number can be represented at the top of the program.

First we made a loop to make sure that MATLAB picks up at least one representation of each number. Then the perms function is used to arrange all the representations of each number except the promoter in all the different ways and call it matrix g.Then you want to find all the rows where the last number of each row of the matrix ends with the number that represents the terminator. Then using the ord function all the different ways of putting the two promoters in the front of each row is developed. Now the program changes the label of the numbers from there number representation number to there edge number where the label goes from 1 to 2 and transposes them. The way that the program lays out the numbers need to be transposed again so we called that matrix sl. Now an if statements were made for the total number of repeats for each row equal to the number of repeats next to each other. The counter is used to find the total number of repeats that are next to each other. For all the number of edges left after all of the repeats are taken out we replaced those with zeros. Now we had to make a vector of ones that will be from 1 to the length of sl. What we call usl is where we get rid of one of the repeated numbers that’s next to each other because one number shows the back half and front half of the gene. Now the new usl is relabeled and includes the numbers for the edges with the promoter at the beginning of each and the terminator at the end of each with the zeros replacing the edges that are after the terminator.

If there is a row in matrix g that does not end with a terminator then we use the command elseif and add a terminator to each of those rows. Since there are two terminators then the program goes through the process one time with the first terminator and another time with the other terminator making these rows longer than if they originally had a terminator at the end. After this whole process all the rows start with a promoter and end with a terminator and have zeros after the terminator is represented.

At the end of the program we print out the total number of arrangements of false positives before the zeros after the terminator are replaced with the extra edges. Also, the rows that are not repeated are printed out. Now the program finds all the rows that have terminators starting in column 8 to 12. We found how many ways we can arrange the remaining edges depending on where the terminator is and take that number and multiply by the amount of times the terminator is in each spot and add them together for each column number. This number gives the number of false positives for a Hamiltonian path.

MATLAB programs used to find the false positives:

[http://gcat.davidson.edu/iGEM07/For_Missouri_Western/fpalmostadelman.m 1. Adelman's False Positives with 12 eges/7nodes]

[http://gcat.davidson.edu/iGEM07/For_Missouri_Western/fpadelman.m 2. Adelman's False Positives with 14 edges/7 nodes]

[http://gcat.davidson.edu/iGEM07/For_Missouri_Western/fpweighter.m 3. Counter Program for Adelman's False Positives]

[http://gcat.davidson.edu/iGEM07/For_Missouri_Western/fpppos6.m 4. False Positives with 9 edges/6 nodes]