Besides HMMs and CRFs, other methods do exist for computational gene identification. Semi-markov models generate variable sequence length emissions, meaning that the transitions are not entirely memory-less on the hidden states.
Max-min models are adaptations of support vector machines. These methods have not yet been applied to mammalian genomes.4
4 For better understanding of SVM: http://dspace.mit.edu/bitstream/hand...663/6-034Fall- 2002/OcwWeb/Electrical-Engineering-and-Computer-Science/6-034Artificial-IntelligenceFall2002/Tools/detail/svmachine.htm