Change emission and transition frequencies to explore the behavior of the Hidden Markov Model
In genomic DNA, CG dinucleotides are often methylated. Methylated Cytosine might change into a Thymine by accidental deamination. As a result of this process, the CG dinucleotide frequency in genomic DNA is often much smaller than expected.
However, methylation is often suppressed in the promoter regions of active genes, and therefore one can find there regions with much higher CG frequency than elsewhere in the genome. Such regions are important signals for gene finding, and they are called CpG islands. Often, CpG islands are modeled by a Hidden Markov Model similar to the Fair Bet Casino Example.