Statistical Analysis of Potential Barriers in Real DNA Sequences

Background:  DNA sequences consist of strings of amino acids labeled A, C, T and G.  Combinations of them produce the proteins necessary for life, but there are different sequences that encode the same proteins.  Although we understand the rules by which the sequences are translated into proteins, there is not yet a complete understanding of the physics of how this occurs.  One model that is used in mathematical biology is the Salerno model.  However, if the Salerno model is an accurate description of reality, then some of the sequences that would theoretically encode a certain protein would not actually work.  According to this “Kasman Effect” (named after a CofC math professor), a “potential barrier” could keep certain sequences from being translated even though standard biological theory suggests that they would.  This effect has already been verified in computer experiments modeling the dynamics of DNA molecules, but it has not yet been explored in real DNA.

Research Problems:  In this project, a student would statistically examine real DNA sequences that are available for download from government websites to determine whether these potential barriers occur less frequently than would be expected if they were not selected against.  Note that Professor Kasman has done some elementary computations based on a small number of downloaded sequences and it appears so far that the answer is that they do occur much less frequently than expected, which suggests that the “effect” is real.  However, the use of more sophisticated statistical analyses and larger data sets is now necessary, and it is hoped that a student researcher would be able to help.

What Courses/Skills Do I Need To Have Taken?  MATH 250 is a minimum prerequisite, but it would be best if the student researcher was familiar with more advanced statistical methodology and had at least some knowledge of basic biology and genetics.

When Can I Work on the Project?  This project could begin any time.

Is Funding Available?  There has been no grant funding set aside for this project, however there may be grants that we can apply for once we formalize a project.

More Information: Please email Prof. Kasman if you are interested in learning more.