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Figure 2 | BMC Bioinformatics

Figure 2

From: Dinucleotide controlled null models for comparative RNA gene prediction

Figure 2

Site dependencies for overlapping dinucleotides (red-gray): The substitution process of a given nucleotide x k at site k by another one depends on the states xk-1, x k , xk+1, the subsequence s k . Q k has the dimension 64 × 64, where only one mutation is allowed at the current site k. The substitution rate for the whole sequence q(x) is the sum of each rate q(k) = Q k (s k , s k ) multiplied with a site-specific scaling factor f k , with k = 1, ..., l.

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