Probability Equation

We tried to modify our model with a probability equation from an article of the National Institute for Mathematical and Biological Synthesis, Knoxville, Tennessee, United States of America published in the internet page PLOSE ONE with the name Is Thermosensing Property of RNA Thermometers Unique? This work looks for the probability of finding a RNA at an openness way using parameters of temperature and time.

This could described the chance of finding our riboswitch k115017 open or closed, because it represented based on their use of parameters a more smooth chance in the fold of the thermosensor.

"Pi(T) is the probability of finding the window at position “i” in a gene, open at temperature (C), ai and bi are the intercept and slope parameters of how the log-odds of finding an open window at position “i”, log(pi(T)/1- pi(T)), changes with temperature. The ratio –ai/bi indicates the temperature at which the probability of openness of a window is 0.5."http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0011308

Our team used the last data of –ai/bi = T when openness is 0.5, to get “ai” expressed in b ( ai= -T*bi) and have our own goods ; to find b the authors of the articles, compared across the 100 genes, found that values were not significantly greater than zero for 24 genes at p value is 0.05, so b value is 0.157. This implies that a small fraction of genes did not show a significant change in openness of its RBS with temperature over the range of temperatures considered. Then we place our control temperature in the isolated equation and get a= -32*0.157 to get the “a” value that was negative 5.024.

But there were some problems using the pi(T) formula in the matlab simulations like malfunction of the equation at the moment of seen graphs or the incorrect insertion of parameters in the simulation, so finally the team decided to leave it apart of the graphics.

We mention this special formula because it was the solution of the fast growth and decrease of the concentrations of the RNAs and proteins in E.coli. We run out of time and it was almost imposible to experiment with it and get better results, but heres the small advance we made with all this.