># # parameters for human version # # date : 1.1.2010 # # # Properties for augustus #------------------------------------ /augustus/verbosity 3 # 0-3, 0: only print the neccessary maxDNAPieceSize 2000000 # maximum segment that is predicted in one piece stopCodonExcludedFromCDS false # make this 'true' if the CDS does do not include the stop codon (both for input and output) # gff output options: protein on # output predicted protein sequence codingseq off # output the coding sequence exonnames off # output 'single', 'initial', 'terminal' or 'internal' for CDS cds on # output 'cds' as feature for exons introns off # output introns start on # output start codons (translation start) stop on # output stop codons (translation stop) tss on # output transcription start site tts on # output transcription termination site print_utr off # output 5'UTR and 3'UTR lines in addition to exon lines gff3 off # output in gff3 format (with exon IDs and Parents) checkExAcc off # internal parameter for extrinsic accuracy # alternative transcripts and posterior probabilities sample 0 # the number of sampling iterations alternatives-from-sampling false # output alternative transcripts minexonintronprob 0.08 # minimal posterior probability of all (coding) exons minmeanexonintronprob 0.4 # minimal geometric mean of the posterior probs of introns and exons maxtracks -1 # 3 # maximum number of transcripts overlapping at the same sequence position (-1: no limit) keep_viterbi true # set to true if all Viterbi transcripts should be reported # mea parameter mea 0 /MeaPrediction/alpha_E 9.375 /MeaPrediction/alpha_I 1.875 /MeaPrediction/x0_E -1.25 /MeaPrediction/x0_I -0.78125 /MeaPrediction/x1_E 5 /MeaPrediction/x1_I 10 /MeaPrediction/y0_E 0.5 /MeaPrediction/y0_I 0.9 #/MeaPrediction/alpha_E 9.375 #/MeaPrediction/alpha_I 1.875 #/MeaPrediction/x0_E -1.25 #/MeaPrediction/x0_I -0.78125 #/MeaPrediction/x1_E 5 #/MeaPrediction/x1_I 10 #/MeaPrediction/y0_E 0.5 #/MeaPrediction/y0_I 0.9 # # Don't mess with any parameters below this point! # They are mainly used for training. # # global constants # ---------------------------- /Constant/trans_init_window 22 /Constant/ass_upwindow_size 33 /Constant/ass_start 3 /Constant/ass_end 2 /Constant/dss_start 3 /Constant/dss_end 4 /Constant/init_coding_len 15 /Constant/intterm_coding_len 5 /Constant/tss_upwindow_size 45 /Constant/decomp_num_at 1 /Constant/decomp_num_gc 1 /Constant/gc_range_min 0.37 /Constant/gc_range_max 0.52 /Constant/decomp_num_steps 2 /Constant/min_coding_len 201 /Constant/probNinCoding 0.23 /Constant/subopt_transcript_threshold 0.86 /Constant/almost_identical_maxdiff 10 GCwinsize 3000 # type of weighing, one of 1 = equalWeights, 2 = gcContentClasses, 3 = multiNormalKernel /BaseCount/weighingType 3 # file with the weight matrix (only for multiNormalKernel type weighing) /BaseCount/weightMatrixFile human_weightmatrix.txt # Properties for IGenicModel # ---------------------------- /IGenicModel/verbosity 3 /IGenicModel/infile human_igenic_probs.pbl /IGenicModel/outfile human_igenic_probs.pbl /IGenicModel/patpseudocount 5.0 /IGenicModel/k 4 tieIgenicIntron true # make igenic content model equal to intron content model # Properties for ExonModel # ---------------------------- /ExonModel/verbosity 3 /ExonModel/infile human_exon_probs.pbl /ExonModel/outfile human_exon_probs.pbl /ExonModel/patpseudocount 5.0 /ExonModel/minPatSum 233.3 /ExonModel/k 4 /ExonModel/etorder 2 /ExonModel/etpseudocount 3 /ExonModel/exonlengthD 3000 /ExonModel/maxexonlength 15000 /ExonModel/slope_of_bandwidth 0.2 /ExonModel/minwindowcount 10 /ExonModel/tis_motif_memory 3 /ExonModel/tis_motif_radius 2 # Properties for IntronModel # ---------------------------- /IntronModel/verbosity 3 /IntronModel/infile human_intron_probs.pbl /IntronModel/outfile human_intron_probs.pbl /IntronModel/patpseudocount 5.0 /IntronModel/k 4 /IntronModel/slope_of_bandwidth 0.4 /IntronModel/minwindowcount 2 /IntronModel/asspseudocount 0.00266 /IntronModel/dsspseudocount 0.0005 /IntronModel/dssneighborfactor 0.00173 #/IntronModel/splicefile human_splicefile.txt /IntronModel/sf_with_motif false /IntronModel/d 584 /IntronModel/ass_motif_memory 3 /IntronModel/ass_motif_radius 3 # Properties for UtrModel # ---------------------------- /UtrModel/verbosity 3 /UtrModel/infile human_utr_probs.pbl /UtrModel/outfile human_utr_probs.pbl /UtrModel/k 4 /UtrModel/utr5patternweight 0.1 /UtrModel/utr3patternweight 0.07 /UtrModel/patpseudocount 1 /UtrModel/tssup_k 0 /UtrModel/tssup_patpseudocount 1 /UtrModel/slope_of_bandwidth 0.1 /UtrModel/minwindowcount 3 /UtrModel/exonlengthD 1000 /UtrModel/maxexonlength 1500 /UtrModel/max3singlelength 5500 /UtrModel/max3termlength 3500 /UtrModel/tss_start 8 /UtrModel/tss_end 5 /UtrModel/tata_start 2 # bases before tata /UtrModel/tata_end 10 # bases starting with first base of tata /UtrModel/d_tss_tata_min 26 # minimal distance between start of tata box (if existent) and tss /UtrModel/d_tss_tata_max 37 # maximal distance between start of tata box (if existent) and tss /UtrModel/d_polyasig_cleavage 22 # the transcription end is predicted this many bases after the polyadenylation signal /UtrModel/d_polya_cleavage_min 10 # In training polyA singals are searched in this /UtrModel/d_polya_cleavage_max 30 # distance range range from the tts (cleavage site). /UtrModel/prob_polya 0.9