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Fig. 3 | BMC Bioinformatics

Fig. 3

From: Red: an intelligent, rapid, accurate tool for detecting repeats de-novo on the genomic scale

Fig. 3

Example of the HMM structure. In this simplified example, the HMM consists of four states: two states representing repeats (R l and R h ) and two states representing non-repeats (N l and N h ). The model has transitions from each state to the other three states. Additionally, there is a transition from each state to itself to allow the model to stay in the same state that generates multiple subsequent scores. The assumption underlying this structure is that repetitive regions consist mainly of high scores interleaved with a small number of low ones; in contrast, non-repetitive regions consist mainly of low scores interleaved with a small number of high ones. States R h and R l generate high and low scores in repetitive regions. States N h and N l generate high and low scores in non-repetitive regions

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