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Member "augustus-3.3.3/config/species/maize/maize_parameters.cfg" (22 May 2019, 4974 Bytes) of package /linux/misc/augustus-3.3.3.tar.gz:


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    1 #
    2 # maize (zea mays) parameters. 
    3 # 
    4 # date : 29.4.2006
    5 #
    6 
    7 #
    8 # Properties for augustus
    9 #------------------------------------
   10 /augustus/verbosity 3     # 0-3, 0: only print the necessary
   11 maxDNAPieceSize    200000 # maximum segment that is predicted in one piece
   12 stopCodonExcludedFromCDS false  # make this 'true' if the CDS includes the stop codon (training and prediction)
   13 
   14 # gff output options:
   15 protein             on    # output predicted protein sequence
   16 codingseq           off    # output the coding sequence
   17 cds                 on     # output 'cds' as feature for exons
   18 start               off    # output start codons (translation start)
   19 stop                off    # output stop codons  (translation stop)
   20 introns             off    # output introns
   21 tss                 on   # output transcription start site
   22 tts                 on   # output transcription termination site
   23 print_utr           off   # output 5'UTR and 3'UTR lines in addition to exon lines
   24 
   25 checkExAcc          off   # internal parameter for extrinsic accuracy
   26 
   27 # alternative transcripts and posterior probabilities
   28 sample                100   # the number of sampling iterations
   29 alternatives-from-sampling false # output suboptimal alternative transcripts based on sampling
   30 alternatives-from-evidence true  # output alternative transcripts based on conflicting hints
   31 minexonintronprob     0.08  # minimal posterior probability of all (coding) exons
   32 minmeanexonintronprob 0.4   # minimal geometric mean of the posterior probs of introns and exons
   33 maxtracks             -1    # maximum number of reported transcripts per gene (-1: no limit)
   34 keep_viterbi          true  # set to true if all Viterbi transcripts should be reported
   35 
   36 #
   37 # 
   38 # The rest of the file contains mainly meta parameters used for training.
   39 #
   40 
   41 # global constants
   42 # ----------------------------
   43 
   44 /Constant/trans_init_window     35
   45 /Constant/ass_upwindow_size     55
   46 /Constant/ass_start             3
   47 /Constant/ass_end               4
   48 /Constant/dss_start             3
   49 /Constant/dss_end               4
   50 /Constant/init_coding_len	0
   51 /Constant/intterm_coding_len	0
   52 /Constant/decomp_num_at         1
   53 /Constant/decomp_num_gc         1
   54 /Constant/gc_range_min		0.35   # This range has an effect only when decomp_num_steps>1. 
   55 /Constant/gc_range_max		0.60   # minimal and maximal percentage of c or g
   56 /Constant/decomp_num_steps      10     # I recommend keeping this to 1 for most species.
   57 /Constant/min_coding_len        201    # no gene with a coding sequence shorter than this is predicted
   58 /Constant/probNinCoding         0.228
   59 /Constant/amberprob             0.284  # Prob(stop codon = tag), if 0 tag is assumed to code for amino acid
   60 /Constant/ochreprob             0.2    # Prob(stop codon = taa), if 0 taa is assumed to code for amino acid
   61 /Constant/opalprob              0.516  # Prob(stop codon = tga), if 0 tga is assumed to code for amino acid
   62 
   63 # type of weighing, one of  1 = equalWeights, 2 = gcContentClasses, 3 = multiNormalKernel
   64 /BaseCount/weighingType    3
   65 # file with the weight matrix (only for multiNormalKernel type weighing)
   66 /BaseCount/weightMatrixFile   maize_weightmatrix.txt # change this to your species if at all necessary
   67 
   68 # Properties for IGenicModel
   69 # ----------------------------
   70 /IGenicModel/verbosity      3
   71 /IGenicModel/infile         maize_igenic_probs.pbl   # change this and the other five filenames *_probs.pbl below to your species
   72 /IGenicModel/outfile        maize_igenic_probs.pbl
   73 /IGenicModel/patpseudocount 5.9
   74 /IGenicModel/k              4
   75 
   76 # Properties for ExonModel
   77 # ----------------------------
   78 /ExonModel/verbosity          3
   79 /ExonModel/infile             maize_exon_probs.pbl
   80 /ExonModel/outfile            maize_exon_probs.pbl
   81 /ExonModel/patpseudocount     5
   82 /ExonModel/minPatSum          586.111111111111
   83 /ExonModel/k                  4
   84 /ExonModel/etorder	      2
   85 /ExonModel/etpseudocount      3
   86 /ExonModel/exonlengthD        2000    # beyond this the distribution is geometric
   87 /ExonModel/maxexonlength      15000
   88 /ExonModel/slope_of_bandwidth 0.325
   89 /ExonModel/minwindowcount     1
   90 /ExonModel/tis_motif_memory   1
   91 /ExonModel/tis_motif_radius   1
   92  
   93 # Properties for IntronModel
   94 # ----------------------------
   95 /IntronModel/verbosity          3
   96 /IntronModel/infile             maize_intron_probs.pbl
   97 /IntronModel/outfile            maize_intron_probs.pbl
   98 /IntronModel/patpseudocount     5.9
   99 /IntronModel/k                  4
  100 /IntronModel/slope_of_bandwidth 0.4
  101 /IntronModel/minwindowcount     4
  102 /IntronModel/asspseudocount     0.01525
  103 /IntronModel/dsspseudocount     0.0002
  104 /IntronModel/dssneighborfactor  0.0001
  105 /IntronModel/splicefile         maize_splicefile.txt # this optional file contains additional windows around splice sites for training, uncomment if you have one
  106 /IntronModel/sf_with_motif	true           # if true the splice file is also used to train the branch point region
  107 /IntronModel/d                  903
  108 /IntronModel/ass_motif_memory   2
  109 /IntronModel/ass_motif_radius   2