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J Mol Evol. 1999 Nov;49(5):691-8.

Toward assigning helical regions in alignments of ribosomal RNA and testing the appropriateness of evolutionary models.

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  • 1Theoretische Chemie, Technische Universität München, Lichtenbergstr. 4, D-85747 Garching, Germany.


We suggest a nucleotide substitution model that takes correlation between base-paired nucleotides into account. The model includes the estimation of the transition-transversion ratio and allows inference of the shape parameter of a discrete gamma distribution to include rate heterogeneity. A Cox-test statistic, applied to a diatom ribosomal RNA alignment, shows that the suggested correlation model explains evolution of the stem region better than usual independence models. Moreover, the Cox-test procedure is extended to shed some light upon the problem of assigning helical regions in a secondary structure based alignment. This approach provides an estimate of the percentage of stem positions that do not appear to be correlated.

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