# # s_aureus parameters. (Staphylococcus aureus) # # date : 21.8.2014 # # # Properties for augustus #------------------------------------ genemodel bacterium # no introns, overlapping genes, etc translation_table 11 # prokaryotic genetic code /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 includes the stop codon (training and prediction) # gff output options: protein on # output predicted protein sequence codingseq off # output the coding sequence cds on # output 'cds' as feature for exons start on # output start codons (translation start) stop on # output stop codons (translation stop) introns on # output introns 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 checkExAcc off # internal parameter for extrinsic accuracy # alternative transcripts and posterior probabilities sample 100 # the number of sampling iterations alternatives-from-sampling false # output alternative suboptimal transcripts alternatives-from-evidence false # output alternative transcripts based on explicit evidence from hints 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 # maximum number of reported transcripts per gene (-1: no limit) keep_viterbi true # set to true if all Viterbi transcripts should be reported uniqueCDS true # don't report transcripts that differ only in the UTR UTR off # predict untranslated regions # # # The rest of the file contains mainly meta parameters used for training. # # global constants # ---------------------------- /Constant/trans_init_window 25 /Constant/ass_upwindow_size 30 /Constant/ass_start 3 /Constant/ass_end 2 /Constant/dss_start 3 /Constant/dss_end 3 /Constant/init_coding_len 4 /Constant/intterm_coding_len 5 /Constant/tss_upwindow_size 45 /Constant/decomp_num_at 1 /Constant/decomp_num_gc 1 /Constant/gc_range_min 0.22 # This range has an effect only when decomp_num_steps>1. /Constant/gc_range_max 0.42 # States the minimal and maximal percentage of c or g /Constant/decomp_num_steps 2 # I recomment keeping this to 1 for most species. /Constant/min_coding_len 61 # no gene with a coding sequence shorter than this is predicted /Constant/probNinCoding 0.23 # divide this by .25 to get a malus for making one masked letter part of the coding sequence /Constant/amberprob 0.067 # Prob(stop codon = tag), if 0 tag is assumed to code for amino acid /Constant/ochreprob 0.678 # Prob(stop codon = taa), if 0 taa is assumed to code for amino acid /Constant/opalprob 0.255 # Prob(stop codon = tga), if 0 tga is assumed to code for amino acid /Constant/subopt_transcript_threshold 0.7 /Constant/almost_identical_maxdiff 10 # 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 s_aureus_weightmatrix.txt # change this to your species if at all neccessary # Properties for IGenicModel # ---------------------------- /IGenicModel/verbosity 0 /IGenicModel/infile s_aureus_igenic_probs.pbl # change this and the other five filenames *_probs.pbl below to your species /IGenicModel/outfile s_aureus_igenic_probs.pbl /IGenicModel/patpseudocount 5.0 /IGenicModel/k 4 # order of the Markov chain for content model, keep equal to /ExonModel/k # Properties for ExonModel # ---------------------------- /ExonModel/verbosity 3 /ExonModel/infile s_aureus_exon_probs.pbl /ExonModel/outfile s_aureus_exon_probs.pbl /ExonModel/patpseudocount 0.5 /ExonModel/minPatSum 233.3 /ExonModel/k 4 # order of the Markov chain for content model /ExonModel/etorder 2 /ExonModel/etpseudocount 3 /ExonModel/exonlengthD 2000 # beyond this the distribution is geometric /ExonModel/maxexonlength 35000 /ExonModel/slope_of_bandwidth 0.1875 /ExonModel/minwindowcount 11 /ExonModel/tis_motif_memory 2 /ExonModel/tis_motif_radius 0 /ExonModel/lenboostL 100 # (single and initial) exons above this length are rewarded /ExonModel/lenboostE 0.035 # by a factor of 1+lenboostE for each base that they are longer # Properties for IntronModel # ---------------------------- /IntronModel/verbosity 0 /IntronModel/infile s_aureus_intron_probs.pbl /IntronModel/outfile s_aureus_intron_probs.pbl /IntronModel/patpseudocount 5.0 /IntronModel/k 4 # order of the Markov chain for content model, keep equal to /ExonModel/k /IntronModel/slope_of_bandwidth 0.4 /IntronModel/minwindowcount 4 /IntronModel/asspseudocount 0.00266 /IntronModel/dsspseudocount 0.0005 /IntronModel/dssneighborfactor 0.00173 #/IntronModel/splicefile s_aureus_splicefile.txt # this optional file contains additional windows around splice sites for training, uncomment if you have one /IntronModel/sf_with_motif false # if true the splice file is also used to train the branch point region /IntronModel/d 100 # constraint: this must be larger than 4 + /Constant/dss_end + /Constant/ass_upwindow_size + /Constant/ass_start /IntronModel/ass_motif_memory 3 /IntronModel/ass_motif_radius 3 # Properties for UtrModel # ---------------------------- /UtrModel/verbosity 3 /UtrModel/infile s_aureus_utr_probs.pbl /UtrModel/outfile s_aureus_utr_probs.pbl /UtrModel/k 4 /UtrModel/utr5patternweight 0.5 /UtrModel/utr3patternweight 0.5 /UtrModel/patpseudocount 1 /UtrModel/tssup_k 0 /UtrModel/tssup_patpseudocount 1 /UtrModel/slope_of_bandwidth 0.2375 /UtrModel/minwindowcount 3 /UtrModel/exonlengthD 800 /UtrModel/maxexonlength 1800 /UtrModel/max3singlelength 2000 /UtrModel/max3termlength 1500 /UtrModel/tss_start 8 /UtrModel/tss_end 5 /UtrModel/tata_start 2 /UtrModel/tata_end 10 /UtrModel/tata_pseudocount 2 /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/polyasig_consensus aataaa # polyadenylation signal training not fully automated yet /UtrModel/d_polyasig_cleavage 14 # the transcription end is predicted this many bases after the polyadenylation signal /UtrModel/d_polya_cleavage_min 7 /UtrModel/d_polya_cleavage_max 19 /UtrModel/prob_polya 0.4 /UtrModel/tts_motif_memory 1