# This file contains the list of meta parameters for the coding regions (CDS) which are subject to optimization. # All other meta 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, 19.12.2006 # /Constant/dss_end "1"-"4" /Constant/dss_start "1"-"3" /Constant/ass_start "1"-"3" /Constant/ass_end "0"-"4" /Constant/ass_upwindow_size "1"-"50" /IntronModel/d "100"-"950" /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"