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Figure 1 | BMC Bioinformatics

Figure 1

From: Methods for estimating human endogenous retrovirus activities from EST databases

Figure 1

The structure of the HMM mixture. The structure of the HMM mixture is shown on the left. Each sub-HMM has the structure shown in the middle. The shaded box is the basic block of the sub-HMM and is repeated length-2 times. It is identical in all sub-HMMs; only the emission distribution of the match state varies between blocks. The emission is either the nucleotide in that position of the HERV sequence or a mismatch. The probabilities for match and mismatch are equal for all blocks. The EEMIT-state emits the low-quality end part.

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