Comparison of RNA-folding structures, in-vivo, in-vitro and in-silico

Abstract

The main objective of the work has been to develop the understanding of the difference between RNA structure probing approaches; in vivo, in vitro and in silico. Similarities and differences between three libraries of data from each of the probing approaches were then studied. The difference between the results was obtained by coverage-plotting of the three datasets and eventually, match and mismatch status of the RNA structural data for the three approaches were tabulated. It was shown that the in vitro and in silico data match for the leader region whereas in vivo data mismatch with the in silico data for the same region. Benchmarking the experimental data with computational data, CDS region data for both in vitro and in vivo show an appropriate match with in silico data. For the trailer region, neither in vitro nor in vivo datasets did match with in silico data. When in vivo and in vitro data were compared, it was observed that CDS and trailer regions match while their leader regions mismatch. In this thesis R coding was used to analyze the data. The source codes are available in the appendix of the thesis as well as an online software development hosting service (https://github.com/hanyroze/RNA-structure).