<p><b>Copyright information:</b></p><p>Taken from "Methods for estimating human endogenous retrovirus activities from EST databases"</p><p>http://www.biomedcentral.com/1471-2105/8/S2/S11</p><p>BMC Bioinformatics 2007;8(Suppl 2):S11-S11.</p><p>Published online 3 May 2007</p><p>PMCID:PMC1892069.</p><p></p>ture 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
