Motivation: The aim of this paper is to present a user-friendly Perl programming language prediction tool for computing RNA folding kinetics. 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 RNA base pairs that are formed and the entropic cost associated with the formation of isolated base pairs. The CWT metric was initially implemented using MATLAB. A Perl implementation is provided in this paper and applied to certain HIV-1 RNA sequences. The purpose of creating the Perl implementation of the CWT metric is to make this measure for RNA folding rates more widely available and easy to use as a bioinformatics tool. A version of the CWT algorithm is provided as a supplement to the paper.
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