Coding Region Recognition and Gene Identification

Granjeon and Tarroux (1995) studied the compositional constraints in introns and exons by using a three-layer network, a binary sequence representation, and three output units to train for intron, exon, and counter-example separately. They found that an efficient learning required a hidden layer, and demonstrated that neural network can detect introns if the counter-examples are preferentially random sequences, and can detect exons if the counter-examples are defined using the probabilities of the second-order Markov chains computed in junk DNA sequences. 

More recently, many integrated programs for gene structure prediction and gene identification have been developed. Several of them, including GRAIL (Uberbacher et 

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