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Figure 5 | BMC Bioinformatics

Figure 5

From: A model-based information sharing protocol for profile Hidden Markov Models used for HIV-1 recombination detection

Figure 5

Detailed calculation of the emission probabilities. Simplified example of the detailed derivation of the emission probabilities from the nucleotide frequencies. At the top, the nucleotide frequencies for each subtype are given and, at the bottom, the emission probabilities derived from these frequencies are provided. In between, for each source combination, the probability of the respective source combination given the nucleotide frequencies is shown on the left side, whereas the emission probabilities of each subtype for the particular source combination is given on the right side. The coloring indicates to which source each subtype belongs for the respective source combination. For example, the third column in the middle block represents the source combination, for which Subtype A and C belong to one source (green) and Subtype B to another (red), yielding emission probabilities of 0.844 and 0.156, respectively, for the green source and of 0.082 and 0.918, respectively, for the red one (we elaborate on some details in this table in the supplements). The simplification made consists of the restriction to 3 subtypes and 2 nucleotides.

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