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.
Oja et al. BMC Bioinformatics 2007 8(Suppl 2):S11 doi:10.1186/1471-2105-8-S2-S11