This week I have been working on installing and understanding a collection of Perl modules called "BioPerl" to help me design a program that can calculate the local and global folding energies of RNA. One class that has been of particular interest to me is the "Bio::Tools::Run::PiseApplication::mfold" class which will hopefully facilitate running Mfold through the Perl script. Another module I have been looking at is "Bio::Align::DNAStatistics" which can calculate several useful statistics about an input sequence such as the number of synonymous and non-synonymous mutations. This module has the potential to be very useful in developing a function that can generate synonymous mutations.
I plan to continue researching BioPerl in search of additional useful modules as well as begin the actual construction of the program to determine exactly what processes need to be done.
I plan to continue researching BioPerl in search of additional useful modules as well as begin the actual construction of the program to determine exactly what processes need to be done.