# 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, 9.5.2008
#

/UtrModel/tss_start             "0"-"12"
/UtrModel/tss_end               "0"-"8"
/UtrModel/prob_polya            "0.0"_"0.3"
/UtrModel/tts_motif_memory      "0"-"2"
/UtrModel/utr5patternweight     "0.4"_"1.0"
/UtrModel/utr3patternweight     "0.5"_"1.0"
/UtrModel/k                     "2"-"4"
/UtrModel/patpseudocount        "1"_"3"
/UtrModel/tssup_k               "0"-"2"
/UtrModel/slope_of_bandwidth    "0.2"_"0.4"
/UtrModel/minwindowcount        "1"-"4"

##/Constant/dss_end		"2"-"4"
#/Constant/dss_start		"1"-"3"
#/Constant/ass_start		"2"-"3"
#/Constant/ass_end		"0"-"3"
#/Constant/ass_upwindow_size	"20"-"30"
#/IntronModel/d                  "80"-"250"
#/IntronModel/ass_motif_memory	"2"-"4"
#/IntronModel/ass_motif_radius	"1"-"4"
#/ExonModel/tis_motif_memory	"0"-"2"
##/ExonModel/tis_motif_radius	"0"-"1"
#/Constant/trans_init_window	"9"-"25"
#/Constant/init_coding_len	"0"-"18"
#/ExonModel/patpseudocount	"2"_"8"
##/ExonModel/etpseudocount	"0"-"10"
##/ExonModel/etorder		"0"-"3"
#/Constant/intterm_coding_len	"0"-"8"
#/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	"0.0001"_"0.001"
#/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"
