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Figure 3 | BMC Bioinformatics

Figure 3

From: Quantifying the relationship between sequence and three-dimensional structure conservation in RNA

Figure 3

"Twilight zone" for RNA sequence alignments. The length of the shorter of the two aligned sequences (N) is plotted against the e-value of aligning both sequences with the Infernal program. (A) Result from an all-against-all sequence comparison of the RNA sequences in the RNA09 dataset. Green dots correspond to true positive relationships (i.e., with -ln(P PID ), -ln(P PSS ), and -ln(P PSI ) higher than 4.5). Blue dots correspond to medium accuracy alignments (i.e., with at least one of the three scores below or equal to 4.5). Orange dots correspond to true negatives relationships (i.e., with -ln(P PID ), -ln(P PSS ), and -ln(P PSI ) lower or equal to 4.5). The inner plot shows the results for alignments with N shorter than 500 nucleotides. (B) The best-fit curve (red line in panels A and B) that optimally separates true positive from true negative. Matthew's correlation coefficient of 0.81 (-Log10(e-value) = 3.11+3.62e+02·e-0.0798N, fitting correlation coefficient 0.85, probability 1.6·10-2).

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