Approaches to gene finding: Generalized hidden Markov models
Each HMM state can be a probabilistic sub-model
Complex hierarchical system
Requires care in modeling state overlaps
Example:
- Genie, Kulp et al. (1996), ISMB, 4, 134-142
- GenScan, Burge and Karlin (1997), JMB, 268(1), 78-94