A gene structure prediction program using duration HMM

Gene structure prediction, which is to predict protein coding regions in a given nucleotide sequence, is a critical process in annotating genes and greatly affects gene analysis and genome annotation. As the gene structure of eukaryotes is much more complicated than that of prokaryotic genes, eukaryotic gene structure prediction should have more diverse and more complicated computational models. We have developed GeneChaser, a gene structure prediction program, using a duration hidden markov model. GeneChaser consists of two major processes, one of which is to train datasets to produce parameter values and the other of which is to predict protein coding regions based on the parameter values. The program predicts multiple genes rather than a single gene from a DNA sequence. To predict the gene structure for a huge chromosomal DNA sequence, it splits the sequence into overlapped fragments and performs prediction process for each fragment. A few computational models were implemented to detect signal patterns and their scanning efficiency was evaluated. Based on a few criteria, its prediction performance was compared with that of a few commonly used programs, GeneID and Morgan.