Perl Implementation Of A Contact-Waiting Time Metric For Rna Folding

Abstract

The aim of this thesis is to create a user-friendly prediction tool for RNA folding kinetics by using the Perl programming language. RNA folding rates can be determined experimentally for RNA sequences of various lengths. However, predicting the folding rates of long sequences can be very difficult, due to the high number of independent computations required. To avoid this problem, different types of folding metrics have been developed for indirectly predicting RNA folding rates. One such metric is the contact-waiting time (CWT) metric. The CWT metric is a measure that correlates well with the natural logarithm of the folding rates of RNA sequences. This metric takes into account the specific energetic contributions of the type of base pairs that are formed and the entropic cost associated with the formation of isolated base pairs. The implementation of the algorithm used to compute the CWT metric is converted from MATLAB to Perl and applied to HIV RNA sequences. The purpose of creating the Perl implementation of the CWT metric is to make the measure more widely available and easy to use as a bioinformatics tool. An executable version of the CWT algorithm is provided as a supplementary file to the thesis.