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Figure 3 | BMC Genomics

Figure 3

From: Widespread signatures of local mRNA folding structure selection in four Dengue virus serotypes

Figure 3

A. Selection matrices for strong / weak folding for wild-type and one corresponding randomized variant in 4 DENV serotypes. Each row in the matrix corresponds to one sequence; columns are positions along the coding region. If sequence i has a suspected MFE related signal (p-value < 0.05) in position j, the entry (i,j) has a value equal to the corresponding FSCI; otherwise it is equal to zero. White horizontal lines separate between sequences belonging to different serotypes (serotypes are ordered from top to bottom, i.e. sequences 1-652 belong to serotype 1; 653-1268 to serotype 2; 1269-1625 to serotype 3 and 1626-1670 to serotype 4). The randomized matrices are comprised of a single randomized variant for each sequence. We can clearly distinguish positions with conserved MFE related signals with different conservation levels in the wild-type, contrasting with a white noise resembling appearance in the randomized variants. B. Robustness of folding signal conservation to folding window size. MFE related signal conservation basing on 39nt folding windows is shown in positions that overlap with MFE conserved signals basing on 78 nt windows along the coding regions of 4 DENV serotypes for strong (red) and weak (green) folding. As many as 80%, 77%, 90%, 92% of conserved signals related to strong folding (red) and 80%, 82%, 85%, 80% conserved signals related to week folding (green) (for serotypes 1 - 4 correspondingly) overlapped with MFE conserved signals identified with respect to a two times larger folding window (78 nt); this overlap was found to be on average 2.5 - 3 folds higher than in random which was based on conservation levels (with respect to 78 nt folding window) in 100 randomized alignments (p-value < 0.01).

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