GenScan Model

The probabilistic model for gene structure as suggested by Berge and Karlin [3], is based on a GHMM (see Figure ).

  

Figure: GenScan Model [3].

The states of the GHMM correspond to the different functional units on a gene, like promoter regions, exon, intron etc. The transition between the states ensure that the order in which the model visits various states is biologically consistent. The states for an intron and an internal exon are subdivided according to phase offset to the codon frames. For $0\leq i\leq 2$, the state I_i (respectively, E_i) corresponds to introns (exons) starting i positions after a codon starts. Note that the only transition from I_i to any internal exon state is to E_i. Also note that the model is divided into two symmetric halves. The upper half of the figure (states with a ``+" superscript) models a gene on the forward strand and the lower half models a gene on the backward strand of the genomic sequence. If the parameters (like $\pi$, a_i,j, etc.) are suitably determined, then the model can be used for gene structure prediction in the following manner.