# This file contains the list of meta parameters for the Untranslated Regions (UTRs), 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 optimization process. # Basically, different values for these meta parameters are tried out and the ones # giving best performance in a cross-validation on the training set are chosen. # 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/prob_polya "0.0"_"0.99" /UtrModel/d_polya_cleavage_min "6"-"14" /UtrModel/d_polya_cleavage_max "17"-"27" /UtrModel/tss_start "0"-"12" /UtrModel/tss_end "0"-"8" /UtrModel/tts_motif_memory "0"-"2" /UtrModel/utr5patternweight "0.1"_"1.0" /UtrModel/utr3patternweight "0.1"_"1.0" /UtrModel/patpseudocount "1"_"3" /UtrModel/tssup_k "0"-"2" /UtrModel/slope_of_bandwidth "0.2"_"0.4" /UtrModel/minwindowcount "1"-"4" #/UtrModel/k "2"-"4"