Structure-Based Alignment and Consensus Secondary Structures for Three HIV-Related RNA Genomes
Fig 2
SHAPE-structure dependent alignment.
(A) SHAPE-directed alignment over one 200-nt window in the RRE. Sequences are numbered relative to the HIV-1 RNA genome, with the transcription start site as +1. (B, C) Windowed linear regression statistics as a function of the HIV-1 (NL4-3) sequence, computed over 200-nt windows. Correlations of SHAPE values across the three-genome sequence alignment were evaluated by F-test (results shown as p-values; black); pairwise comparisons with HIV-1 were evaluated by t-test (results shown as p-values). The entire HIV-1 alignment is shown; RNA landmarks are given at the bottom of the figure.