# # Transition probabilities and initial Probabilities for the overall HMM # # number of states 24 # # Transition probabilities of the Generalised Hidden-Markov Model # Date: 19.05.2003 # Initial probabilities (a priori probs for a state ending at a # certain position, e.g. the position before the first nukleotide in # the sequence or the last position. # only non-zero probabilities [Initial] # number of states where a start is possible 24 # state prob statename 0 .92 # start intergenic region 1 .001 # single Exon 2 .001 # initial Exon win 0 3 .001 # initial Exon win 1 4 .001 # initial Exon win 2 5 .001 # internal Exon win 0 6 .001 # internal Exon win 1 7 .001 # internal Exon win 2 8 .001 # terminal exon 9 .001 # lessD0 Intron win 0 10 .001 # 11 .001 # 12 .02 # geometric0 Intron win 0 13 .001 # 14 .001 # 15 .001 # 16 .001 # 17 .02 # geometric1 Intron win 1 18 .001 # 19 .001 # 20 .001 # 21 .001 # 22 .02 # geometric2 Intron win 2 23 .001 # # Terminal probabilities (a priori probs for a state ending at # the last position. # only non-zero probabilities neccessary [Terminal] # number of states where terminating is possible 24 # state prob statename 0 .92 # start intergenic region 1 .001 # single Exon 2 .001 # initial Exon win 0 3 .001 # initial Exon win 1 4 .001 # initial Exon win 2 5 .001 # internal Exon win 0 6 .001 # internal Exon win 1 7 .001 # internal Exon win 2 8 .001 # terminal exon 9 .001 # lessD0 Intron win 0 10 .001 # 11 .001 # 12 .02 # geometric0 Intron win 0 13 .001 # 14 .001 # 15 .001 # 16 .001 # 17 .02 # geometric1 Intron win 1 18 .001 # 19 .001 # 20 .001 # 21 .001 # 22 .02 # geometric2 Intron win 2 23 .001 # # # Transition probabilities # only non-zero probabilities [Transition] # ----- Igenic region ----- # intergenic region 0 0 .9999 # single 0 1 .000017 # initial exon 0, 40% of the multi exon genes 0 2 .000028 # initial exon 1, 43% of the multi exon genes 0 3 .000028 # initial exon 2, 17% of the multi exon genes 0 4 .000027 # ----- Single Exon ----- # Final Intergenic region 1 0 1.0 # ----- Initial Exon 0 ----- # longdss0 Intron 2 10 1.0 # ----- Initial Exon 1 ----- # longdss1 Intron 3 15 1.0 # ----- Initial Exon 2 ----- # longdss2 Intron 4 20 1.0 # ----- Internal Exon 0 ----- # longdss0 Intron 5 10 1.0 # ----- Internal Exon 1 ----- # longdss1 Intron 6 15 1.0 # ----- Internal Exon 2 ----- # longdss2 Intron 7 20 1.0 # ----- Terminal Exon ----- # intergenic region 8 0 1 # ----- lessD0 Intron 0 ----- # longass0 9 13 1.0 # ----- longdss0 Intron 0 ----- # lessD0 10 9 .5 # equalD0 10 11 .5 # ----- equalD0 Intron 0 ----- # geometric0 11 12 1.0 # ----- geometric0 Intron 0 ----- # geometric0 intron 12 12 .9997447 # longass0 12 13 .0002553 # ----- longass0 Intron 0 ----- # internal exon 0, 45% of all internal exons 13 5 .3 # internal exon 1, 33% of all internal exons 13 6 .3 # internal exon 2, 22% of all internal exons 13 7 .3 # terminal exon 13 8 .1 # ----- lessD1 Intron 1 ----- # longass1 14 18 1.0 # ----- longdss1 Intron 1 ----- # lessD1 15 14 .5 # equalD1 15 16 .5 # ----- equalD1 Intron 1 ----- # geometric1 16 17 1.0 # ----- geometric1 Intron 1 ----- # geometric1 intron 17 17 .9997447 # longass1 17 18 .0002553 # ----- longass1 Intron 1 ----- # internal exon 0, 45% of all internal exons 18 5 .3 # internal exon 1, 33% of all internal exons 18 6 .3 # internal exon 2, 22% of all internal exons 18 7 .3 # terminal exon 18 8 .1 # ----- lessD2 Intron 2 ----- # longass2 19 23 1.0 # ----- longdss2 Intron 2 ----- # lessD2 20 19 .5 # equalD2 20 21 .5 # ----- equalD2 Intron 2 ----- # geometric0 21 22 1.0 # ----- geometric2 Intron 2 ----- # geometric2 intron 22 22 .9997447 # longass2 22 23 .0002553 # ----- longass2 Intron 2 ----- # internal exon 0, 45% of all internal exons 23 5 .3 # internal exon 1, 33% of all internal exons 23 6 .3 # internal exon 2, 22% of all internal exons 23 7 .3 # terminal exon 23 8 .1