RNA sequence evolution with secondary structure constraints: comparison of substitution rate models using maximum-likelihood methods.

@article{Savill2001RNASE,
  title={RNA sequence evolution with secondary structure constraints: comparison of substitution rate models using maximum-likelihood methods.},
  author={Nicholas J. Savill and David C. Hoyle and Paul G. Higgs},
  journal={Genetics},
  year={2001},
  volume={157 1},
  pages={
          399-411
        }
}
We test models for the evolution of helical regions of RNA sequences, where the base pairing constraint leads to correlated compensatory substitutions occurring on either side of the pair. These models are of three types: 6-state models include only the four Watson-Crick pairs plus GU and UG; 7-state models include a single mismatch state that combines all of the 10 possible mismatches; 16-state models treat all mismatch states separately. We analyzed a set of eubacterial ribosomal RNA… CONTINUE READING

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