# # configuration file for the model architecture # with shadow states for simultaneous prediction of genes on BOTH STRANDS # contains states for both UTRs, including variable length UTR introns # date : 14.10.2006 # # # Training States # # order should be igenic and intron before utr and exon /EHMMTraining/statecount 4 /EHMMTraining/state00 igenicmodel /EHMMTraining/state01 exonmodel /EHMMTraining/state02 intronmodel /EHMMTraining/state03 utrmodel # Properties for NamGene # ---------------------------- /NAMGene/SynchState 0 /NAMGene/statecount 71 /NAMGene/state00 igenicmodel # intergenic region /NAMGene/state01 exonmodel # single Exon /NAMGene/state02 exonmodel # initial Exon win 0 /NAMGene/state03 exonmodel # initial Exon win 1 /NAMGene/state04 exonmodel # initial Exon win 2 /NAMGene/state05 exonmodel # internal Exon win 0 /NAMGene/state06 exonmodel # internal Exon win 1 /NAMGene/state07 exonmodel # internal Exon win 2 /NAMGene/state08 exonmodel # terminal exon /NAMGene/state09 intronmodel # lessD0 Intron win 0 /NAMGene/state10 intronmodel # longdss0 /NAMGene/state11 intronmodel # equalD0 Intron win 0 /NAMGene/state12 intronmodel # geometric0 Intron win 0 /NAMGene/state13 intronmodel # longass0 /NAMGene/state14 intronmodel # lessD1 Intron win 1 /NAMGene/state15 intronmodel # longdss1 /NAMGene/state16 intronmodel # equalD1 Intron win 1 /NAMGene/state17 intronmodel # geometric1 Intron win 1 /NAMGene/state18 intronmodel # longass1 /NAMGene/state19 intronmodel # lessD2 Intron win 2 /NAMGene/state20 intronmodel # longdss2 /NAMGene/state21 intronmodel # equalD2 Intron win 2 /NAMGene/state22 intronmodel # geometric2 Intron win 2 /NAMGene/state23 intronmodel # longass2 /NAMGene/state24 utrmodel # 5' UTR single exon /NAMGene/state25 utrmodel # 5' UTR initial exon /NAMGene/state26 utrmodel # 5' UTR intron single base /NAMGene/state27 utrmodel # 5' UTR intron variable length /NAMGene/state28 utrmodel # 5' UTR internal exon /NAMGene/state29 utrmodel # 5' UTR terminal exon /NAMGene/state30 utrmodel # 3' UTR single exon /NAMGene/state31 utrmodel # 3' UTR initial exon /NAMGene/state32 utrmodel # 3' UTR intron single base /NAMGene/state33 utrmodel # 3' UTR intron variable length /NAMGene/state34 utrmodel # 3' UTR internal exon /NAMGene/state35 utrmodel # 3' UTR terminal exon /NAMGene/state36 exonmodel # reverse single Exon /NAMGene/state37 exonmodel # reverse initial /NAMGene/state38 exonmodel # reverse internal Exon win 0 /NAMGene/state39 exonmodel # reverse internal Exon win 1 /NAMGene/state40 exonmodel # reverse internal Exon win 2 /NAMGene/state41 exonmodel # reverse terminal exon win 0 /NAMGene/state42 exonmodel # reverse terminal exon win 1 /NAMGene/state43 exonmodel # reverse terminal exon win 2 /NAMGene/state44 intronmodel # reverse lessD0 Intron win 0 /NAMGene/state45 intronmodel # reverse longdss0 /NAMGene/state46 intronmodel # reverse equalD0 Intron win 0 /NAMGene/state47 intronmodel # reverse geometric0 Intron win 0 /NAMGene/state48 intronmodel # reverse longass0 /NAMGene/state49 intronmodel # reverse lessD1 Intron win 1 /NAMGene/state50 intronmodel # reverse longdss1 /NAMGene/state51 intronmodel # reverse equalD1 Intron win 1 /NAMGene/state52 intronmodel # reverse geometric1 Intron win 1 /NAMGene/state53 intronmodel # reverse longass1 /NAMGene/state54 intronmodel # reverse lessD2 Intron win 2 /NAMGene/state55 intronmodel # reverse longdss2 /NAMGene/state56 intronmodel # reverse equalD2 Intron win 2 /NAMGene/state57 intronmodel # reverse geometric2 Intron win 2 /NAMGene/state58 intronmodel # reverse longass2 /NAMGene/state59 utrmodel # reverse 5' UTR single exon /NAMGene/state60 utrmodel # reverse 5' UTR initial exon /NAMGene/state61 utrmodel # reverse 5' UTR intron single base /NAMGene/state62 utrmodel # reverse 5' UTR intron variable length /NAMGene/state63 utrmodel # reverse 5' UTR internal exon /NAMGene/state64 utrmodel # reverse 5' UTR terminal exon /NAMGene/state65 utrmodel # reverse 3' UTR single exon /NAMGene/state66 utrmodel # reverse 3' UTR initial exon /NAMGene/state67 utrmodel # reverse 3' UTR intron single base /NAMGene/state68 utrmodel # reverse 3' UTR intron variable length /NAMGene/state69 utrmodel # reverse 3' UTR internal exon /NAMGene/state70 utrmodel # reverse 3' UTR terminal exon # Properties for IGenicModel # ---------------------------- /IGenicModel/type00 igenic # Properties for ExonModel # ---------------------------- /ExonModel/type00 single /ExonModel/type01 initial0 /ExonModel/type02 initial1 /ExonModel/type03 initial2 /ExonModel/type04 internal0 /ExonModel/type05 internal1 /ExonModel/type06 internal2 /ExonModel/type07 terminal /ExonModel/type08 rsingle /ExonModel/type09 rinitial /ExonModel/type10 rinternal0 /ExonModel/type11 rinternal1 /ExonModel/type12 rinternal2 /ExonModel/type13 rterminal0 /ExonModel/type14 rterminal1 /ExonModel/type15 rterminal2 # Properties for IntronModel # ---------------------------- /IntronModel/type00 lessD0 /IntronModel/type01 longdss0 /IntronModel/type02 equalD0 /IntronModel/type03 geometric0 /IntronModel/type04 longass0 /IntronModel/type05 lessD1 /IntronModel/type06 longdss1 /IntronModel/type07 equalD1 /IntronModel/type08 geometric1 /IntronModel/type09 longass1 /IntronModel/type10 lessD2 /IntronModel/type11 longdss2 /IntronModel/type12 equalD2 /IntronModel/type13 geometric2 /IntronModel/type14 longass2 /IntronModel/type15 rlessD0 /IntronModel/type16 rlongdss0 /IntronModel/type17 requalD0 /IntronModel/type18 rgeometric0 /IntronModel/type19 rlongass0 /IntronModel/type20 rlessD1 /IntronModel/type21 rlongdss1 /IntronModel/type22 requalD1 /IntronModel/type23 rgeometric1 /IntronModel/type24 rlongass1 /IntronModel/type25 rlessD2 /IntronModel/type26 rlongdss2 /IntronModel/type27 requalD2 /IntronModel/type28 rgeometric2 /IntronModel/type29 rlongass2 # Properties for UtrModel # ---------------------------- /UtrModel/type00 utr5single /UtrModel/type01 utr5init /UtrModel/type02 utr5intron /UtrModel/type03 utr5intronvar /UtrModel/type04 utr5internal /UtrModel/type05 utr5term /UtrModel/type06 utr3single /UtrModel/type07 utr3init /UtrModel/type08 utr3intron /UtrModel/type09 utr3intronvar /UtrModel/type10 utr3internal /UtrModel/type11 utr3term /UtrModel/type12 rutr5single /UtrModel/type13 rutr5init /UtrModel/type14 rutr5intron /UtrModel/type15 rutr5intronvar /UtrModel/type16 rutr5internal /UtrModel/type17 rutr5term /UtrModel/type18 rutr3single /UtrModel/type19 rutr3init /UtrModel/type20 rutr3intron /UtrModel/type21 rutr3intronvar /UtrModel/type22 rutr3internal /UtrModel/type23 rutr3term