For gene finding in Humans or other eukaryotes the story is further complicated
by the exon/intron structure. A general schematic for this is shown in figure 5,
page 
, where each of the states represents another HMM
(which we don't specify here). See [6,7,5] for more detailed
HMM's, some of which include fixes to allow for possible insertions and deletions in
the sequence.
Figure 5: An HMM for modeling eukaryotic genes, allowing for exon/intron structure. Each
of the states can be an HMM or some other statistical model.