# This file contains the list of meta parameters which are subject to optimization. 
# All other parameters are chosen as given in the species parameter file. The order 
# of the parameters determines the order in the optimisation process.
# For each parameter the range of possible values is specified after the parameter
# name and at least one white space.
# 3 cases are possible for the range:
# - an explicit list is given, e.g. protein	"on" "off"
# - it is an integer range, e.g. window_size	"1"-"5"
# - it is a range of floating point numbers, e.g. pseudocount	"0.3"_"1.8"
#
# 
# Mario Stanke, 23.08.2005
#

/UtrModel/utr3patternweight     "0.0"_"1.0"
/UtrModel/utr5patternweight     "0.0"_"0.2"
/UtrModel/tata_pseudocount      "1"-"3"
#/UtrModel/patpseudocount        "0.5"_"8"
#/UtrModel/slope_of_bandwidth    "0.05"_"0.3"
#/UtrModel/tssup_k               "0"-"3"
#/UtrModel/tssup_patpseudocount  "0.5"_"5"
#/UtrModel/minwindowcount        "2"-"6"
#/UtrModel/d_polya_cleavage_min  "2"-"10"
#/UtrModel/d_polya_cleavage_max  "15"-"25"
#/UtrModel/tss_start             "5"-"8"  
#/UtrModel/tss_end               "5"  
#/UtrModel/tata_start            "0"-"4"
#/UtrModel/tata_end              "6"-"12"
#/Constant/tss_upwindow_size     "10"-"50"
#/Constant/dss_end		"1"-"4"
#/Constant/dss_start		"1"-"3"
#/Constant/ass_start		"1"-"3"
#/Constant/ass_end		"0"-"4"
#/Constant/ass_upwindow_size	"2"-"40"
#/IntronModel/d                  "100"-"800"
#/IntronModel/ass_motif_memory	"0"-"3"
#/IntronModel/ass_motif_radius	"0"-"4"
#/ExonModel/tis_motif_memory	"0"-"3"
#/ExonModel/tis_motif_radius	"0"-"3"
#/Constant/trans_init_window	"0"-"25"
#/Constant/init_coding_len	"0"-"18"
#/ExonModel/patpseudocount	"0.5"_"5"
#/ExonModel/etpseudocount	"0"-"10"
#/ExonModel/etorder		"0"-"3"
#/Constant/intterm_coding_len	"0"-"13"
#/ExonModel/slope_of_bandwidth	"0.05"_"0.6"
#/ExonModel/minwindowcount	"1"-"15"
#/IGenicModel/patpseudocount	"0.5"_"7"
#/IntronModel/patpseudocount	"0.5"_"7"
#/IntronModel/slope_of_bandwidth	"0.05"_"0.6"
#/IntronModel/minwindowcount	"1"-"8"
#/IntronModel/asspseudocount	"0.0005"_"0.03"
#/IntronModel/dsspseudocount	"0.0002"_"0.04"
#/IntronModel/dssneighborfactor  "0.0001"_"0.01"
#/ExonModel/minPatSum		"100"_"600"
#/Constant/probNinCoding         "0.15"_".25"
#/Constant/decomp_num_steps	"1"-"5"
# comment parameters out that you do not want to be subject of optimization
#/IGenicModel/k                  "4" "3" "5"
#/IntronModel/k                  "4" "3" "5"
#/ExonModel/k                    "4" "3" "5"
