Fig. 4

The state diagram of GPRED-GC. The states beginning with r represents the reverse strand. \(E^{\mathrm {H}}_{\text {single}}\): a single exon of high GC content. \(E^{\mathrm {M}}_{\text {single}}\): a single exon of medium GC content. \(E^{\mathrm {L}}_{\text {single}}\): a single exon of low GC content. E_{init H}: the initial coding exon of a multi-exon gene with high GC content. E_{init M} : the initial exon of a multi-exon gene with medium GC content. E_{init L}: the initial exon of a multi-exon gene with low GC content. DSS: a donor splice site. I_short: an intron emitting at most d nucleotides. I_fixed: a longer intron with the first d nucleotides. I_geo: a longer intron emitting one nucleotide at a time after the first d nucleotides. ASS: an acceptor splice site with branch point. E_H: an internal coding exon of a multi-exon gene with high GC content. E_M: the internal exon of a multi-exon gene with medium GC content. E_L: the internal exon of a multi-exon gene with low GC content. \(E^{\mathrm {H}}_{\text {term}}\): the last coding exon of a multi-exon gene with high GC content. \(E^{\mathrm {M}}_{\text {term}}\): the terminal exon of a multi-exon gene with medium GC content. \(E^{\mathrm {L}}_{\text {term}}\): the terminal exon of a multi-exon gene with low GC content. IR: intergenic region. Diamonds represent the states that emit fixed length strings. Ovals represent the states including explicit length distribution. The numbers at the arrows show the transition probabilities. The transition probabilities incident to new exon states are derived using equal divisions (strategy 1). The exponents 0, 1, and 2 represent the reading frame phase. For an exon state, this is the position of the last base of the exon in its codon. For the other states, the exponent are the preceding-exon phase. The small circles represent silent states