# # Transition probabilities and initial Probabilities for the overall HMM # # number of states 48 # # 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 1 # state prob statename 0 1.0 # intergenic region # 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 1 # state prob statename 47 1.0 # intergenic region # # Transition probabilities # only non-zero probabilities [Transition] # ----- Igenic region ----- # intergenic region 0 0 .9999 # single 0 1 .000009 # initial exon 0, 40% of the multi exon genes 0 2 .000014 # initial exon 1, 43% of the multi exon genes 0 3 .000014 # initial exon 2, 17% of the multi exon genes 0 4 .000013 # reverse single exon 0 24 .000009 # reverse terminal exon 0 0 29 .000014 # reverse terminal exon 1 0 30 .000014 # reverse terminal exon 2 0 31 .000013 # ----- Single Exon ----- # Final Intergenic region 1 47 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 47 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 # # ------------------------ reverse strand -------------------------- # # ----- reverse Single Exon ----- # Intergenic region 24 47 1.0 # ----- reverse Initial Exon ----- # Intergenic region 25 47 1 # ----- reverse Internal Exon 0 ----- # reverse longass0 26 36 1.0 # ----- reverse Internal Exon 1 ----- # reverse longass1 27 41 1.0 # ----- reverse Internal Exon 2 ----- # reverse longass2 28 46 1.0 # ----- reverse Terminal Exon 0 ----- # reverse longass0 29 36 1.0 # ----- reverse Terminal Exon 1 ----- # reverse longass1 30 41 1.0 # ----- reverse Terminal Exon 2 ----- # reverse longass2 31 46 1.0 # ----- reverse lessD0 Intron 0 ----- # longdss0 32 33 1.0 # ----- reverse longdss0 Intron 0 ----- # reverse internal exon 0, 45% of all internal exons 33 26 .3 # reverse internal exon 1, 33% of all internal exons 33 27 .3 # reverse internal exon 2, 22% of all internal exons 33 28 .3 # reverse initial exon 33 25 .1 # ----- reverse equalD0 Intron 0 ----- # reverse geometric0 34 35 1.0 # ----- reverse geometric0 Intron 0 ----- # reverse geometric0 intron 35 35 .9997447 # reverse longdss0 35 33 .0002553 # ----- reverse longass0 Intron 0 ----- # reverse intron equalD0 36 34 .5 # reverse intron lessD0 36 32 .5 # ----- reverse lessD1 Intron 1 ----- # longdss1 37 38 1.0 # ----- reverse longdss1 Intron 1 ----- # reverse internal exon 0, 45% of all internal exons 38 26 .3 # reverse internal exon 1, 33% of all internal exons 38 27 .3 # reverse internal exon 2, 22% of all internal exons 38 28 .3 # reverse initial exon 38 25 .1 # ----- reverse equalD1 Intron 1 ----- # reverse geometric1 39 40 1.0 # ----- reverse geometric1 Intron 1 ----- # reverse geometric1 intron 40 40 .9997447 # reverse longdss1 40 38 .0002553 # ----- reverse longass1 Intron 1 ----- # reverse intron equalD1 41 39 .5 # reverse intron lessD1 41 37 .5 # ----- reverse lessD2 Intron 2 ----- # longdss2 42 43 1.0 # ----- reverse longdss2 Intron 2 ----- # reverse internal exon 0, 45% of all internal exons 43 26 .3 # reverse internal exon 1, 33% of all internal exons 43 27 .3 # reverse internal exon 2, 22% of all internal exons 43 28 .3 # reverse initial exon 43 25 .1 # ----- reverse equalD2 Intron 2 ----- # reverse geometric2 44 45 1.0 # ----- reverse geometric2 Intron 2 ----- # reverse geometric2 intron 45 45 .9997447 # reverse longdss2 45 43 .0002553 # ----- reverse longass2 Intron 2 ----- # reverse intron equalD2 46 44 .5 # reverse intron lessD2 46 42 .5 # ----- End Igenic region ----- # intergenic region 47 47 .9999 # single 47 1 .000009 # initial exon 0, 40% of the multi exon genes 47 2 .000014 # initial exon 1, 43% of the multi exon genes 47 3 .000014 # initial exon 2, 17% of the multi exon genes 47 4 .000013 # reverse single exon 47 24 .000009 # reverse terminal exon 0 47 29 .000014 # reverse terminal exon 1 47 30 .000014 # reverse terminal exon 2 47 31 .000013