This past week, I have been examining how well we can predict the total folding energy of RNA. I have been using a program called Mfold which predicts the secondary structure of RNA using thermodynamic methods. I began by folding an entire RNA molecule (Rattus rattus CCR5 gene, CCR5-G allele cds) and recording the total folding energy. Then, I broke the sequence into smaller sequences, 30bps longs (30-mers), and determined their individual folding energies. I recorded my results in a Microsoft Excel spreadsheet to help identify how well the global energy correlates with the local energy.
Being these calculations are tedious and cumbersome, I plan to develop a Perl program that can automate this procedure and output the local energies of the k-mers of a given RNA sequence. Moreover, I plan to modify the RNA sequences by making synonymous changes and examining how these changes affect both the local and global folding energies.
I have also continued practicing programming in Perl by creating a program that can take either a DNA or RNA sequence and convert it to its respective amino acid translation. However, I have found that there exists Perl tools called "BioPerl" that are designed to aid in the development of biological programs like these. In the following weeks I plan to better familiarize myself with BioPerl in the hopes that it can be of some use in our research.
Being these calculations are tedious and cumbersome, I plan to develop a Perl program that can automate this procedure and output the local energies of the k-mers of a given RNA sequence. Moreover, I plan to modify the RNA sequences by making synonymous changes and examining how these changes affect both the local and global folding energies.
I have also continued practicing programming in Perl by creating a program that can take either a DNA or RNA sequence and convert it to its respective amino acid translation. However, I have found that there exists Perl tools called "BioPerl" that are designed to aid in the development of biological programs like these. In the following weeks I plan to better familiarize myself with BioPerl in the hopes that it can be of some use in our research.