#
# parameters for Nicotiana tabacum
# 
# date : October 20th, 2005
#

#
# Properties for augustus
#------------------------------------
/augustus/verbosity 3     # 0-3, 0: only print the neccessary

stopCodonExcludedFromCDS false  # make this 'true' if the CDS in the training set do not include the stop codon
UTR on                       # predict 5'UTR

# 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              50    # the number of sampling iterations
alternatives-from-sampling false # output suboptimal alternative transcripts based on sampling
alternatives-from-evidence true  # output alternative transcripts based on conflicting hints
minexonprob         0.3   # minimal posterior probability of all (coding) exons
minmeanstateprob    0.0   # minimal geometric mean of the posterior probs of introns and exons
maxtranscripts      - 1   # maximum number of reported transcripts per gene (-1: no limit)


#
# Don't mess with any parameters below this point!
# They are mainly used for training.

# global constants
# ----------------------------

/Constant/trans_init_window     4
/Constant/ass_upwindow_size     50
/Constant/ass_start             1
/Constant/ass_end               3
/Constant/dss_start             2
/Constant/dss_end               4
/Constant/init_coding_len	0
/Constant/intterm_coding_len	2
/Constant/tss_upwindow_size     45
/Constant/decomp_num_at         1
/Constant/decomp_num_gc         1
/Constant/gc_range_min		0.30
/Constant/gc_range_max		0.41
/Constant/decomp_num_steps      1
/Constant/min_coding_len        201
/Constant/probNinCoding         0.23

# 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   tobacco_weightmatrix.txt

# Properties for IGenicModel
# ----------------------------
/IGenicModel/verbosity      0
/IGenicModel/infile         tobacco_igenic_probs.pbl
/IGenicModel/outfile        tobacco_igenic_probs.pbl
/IGenicModel/patpseudocount 1.58
/IGenicModel/k              4

# Properties for ExonModel
# ----------------------------
/ExonModel/verbosity          3
/ExonModel/infile             tobacco_exon_probs.pbl
/ExonModel/outfile            tobacco_exon_probs.pbl
/ExonModel/patpseudocount     3
/ExonModel/minPatSum          500
/ExonModel/k                  4
/ExonModel/etorder	      2
/ExonModel/etpseudocount      3
/ExonModel/exonlengthD        3000
/ExonModel/maxexonlength      5000
/ExonModel/slope_of_bandwidth 0.26
/ExonModel/minwindowcount     1
/ExonModel/tis_motif_memory   3
/ExonModel/tis_motif_radius   3
 
# Properties for IntronModel
# ----------------------------
/IntronModel/verbosity          0
/IntronModel/infile             tobacco_intron_probs.pbl
/IntronModel/outfile            tobacco_intron_probs.pbl
/IntronModel/patpseudocount     1.6
/IntronModel/k                  4
/IntronModel/slope_of_bandwidth 0.23
/IntronModel/minwindowcount     5
/IntronModel/asspseudocount     0.015
/IntronModel/dsspseudocount     0.000001
/IntronModel/dssneighborfactor  0.01
#/IntronModel/splicefile        tobacco_splicefile.txt
/IntronModel/sf_with_motif	false
/IntronModel/d                  737
/IntronModel/ass_motif_memory   1
/IntronModel/ass_motif_radius   2

# Properties for UtrModel
# ----------------------------
/UtrModel/verbosity             3
/UtrModel/infile                tobacco_utr_probs.pbl
/UtrModel/outfile               tobacco_utr_probs.pbl
/UtrModel/k                     3
/UtrModel/patpseudocount        1
/UtrModel/tssup_k               0
/UtrModel/tssup_patpseudocount  1
/UtrModel/slope_of_bandwidth    0.1
/UtrModel/minwindowcount        3
/UtrModel/exonlengthD           200
/UtrModel/maxexonlength         700
/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
