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Figure S4: Site-Specific Substitution Rate Versus Sequence Entropy for All Sites of 9 Proteins. The Selection Model Is WT, the Mutation Model Is Codon-Based, With Parameters Separately Optimized for Each Protein
doi 10.7717/peerj.5549/supp-4
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Figure S3: Site-Specific Substitution Rate Versus Sequence Entropy for All Sites of 9 Proteins. The Selection Model Is MF, the Mutation Model Is Codon-Based, With Parameters Optimized for Each Protein Separately
Figure S2: Site-Specific Substitution Rate Versus Sequence Entropy for All Sites of Nine Randomly Chosen Proteins. The Selection Model Is WT, the Mutation Model Is Based on the Empirical Flux
Figure S1: Site-Specific Substitution Rate Versus Sequence Entropy for All Sites of Nine Randomly Chosen Proteins. The Selection Model Is MF, the Mutation Model Is Based on the Empirical Flux
Figure 3: Each Point Represents the Substitution Rate Versus the Sequence Entropy for All Sites of the Ribonuclease Protein With PDB Code 1pyl, Which Is Representative of Our Data Set and Makes the Figure Easier to Interpret Because of Its Small Number of Sites.
Figure 6: Each Point Represents a Set of Protein Sites With Similar Hydrophobicity in the Evolutionary Model.
Table S4: Mixed-Effects Model Fit by REML for Each Assemblage and Each Variable
A Site Specific Model and Analysis of the Neutral Somatic Mutation Rate in Whole-Genome Cancer Data
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Figure 5: Violin Plots of the AICc Weights for Each Model.
The Temperature Dependence of Salt-Protein Association Is Sequence Specific
