Computationally annotated RNA noncoding elements from the HIV-1 genome with corresponding entropy Z-scores.

Running cmscan from Infernal 1.1 [53] on the HIV-1 genome (GenBank AF033819.3), we obtain 11 noncoding elements as listed in the table, along with the nucleotide beginning and ending positions, length of noncoding element, E-score, and entropy Z-score. Entropy Z-scores were computed using RNAentropy as explained in the text. Many of the annotated noncoding elements are much shorter than 100 nt, the length of the window size used; however, sporadic checking of entropy Z-scores computed for a moving window of size 50 does not seem to radically change the entropy Z-scores. Nevertheless, certain elements have low entropies and corresponding entropy Z-scores, such as the 5′-UTR and TAR (trans-activation response) element, both of which are known to be involved in the packaging of the HIV-1 genome in the viral capsid [54].