State-transition diagram of the GHMM-based gene finder GeneZilla. Green states were differentially included for the feature-state experiments. Reverse-strand states have been omitted for brevity. A, acceptor site; AATAAA, polyadenylation signal (including ATTAAA); ATG, start codon; b, branch point; CAP, cap site; CpG, CpG island; D, donor site; E, exon; I, intron; N, intergenic; sigP, signal peptide; TATA, TATA box; TAG, stop codon (including TAA and TGA); UTR, untranslated region.
Allen et al. Genome Biology 2006 7(Suppl 1):S9 doi:10.1186/gb-2006-7-s1-s9