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Source code changes of the file "config/species/pisaster/pisaster_parameters.cfg" between
augustus-3.3.2.tar.gz and augustus-3.3.3.tar.gz

About: AUGUSTUS is a program that predicts genes in eukaryotic genomic sequences.

pisaster_parameters.cfg  (augustus-3.3.2):pisaster_parameters.cfg  (augustus-3.3.3)
# #
# pisaster parameters. (Pisaster ochraceus, ochre starfish) # pisaster parameters. (Pisaster ochraceus, ochre starfish)
# #
# date : 2018 # date : 2018
# #
# #
# Properties for augustus # Properties for augustus
#------------------------------------ #------------------------------------
/augustus/verbosity 3 # 0-3, 0: only print the neccessary /augustus/verbosity 3 # 0-3, 0: only print the necessary
maxDNAPieceSize 500000 # maximum segment that is predicted in one piece maxDNAPieceSize 500000 # maximum segment that is predicted in one piece
stopCodonExcludedFromCDS false # make this 'true' if the CDS does not include th e stop codon (training and prediction) stopCodonExcludedFromCDS false # make this 'true' if the CDS does not include th e stop codon (training and prediction)
# gff output options: # gff output options:
protein on # output predicted protein sequence protein on # output predicted protein sequence
codingseq off # output the coding sequence codingseq off # output the coding sequence
cds on # output 'cds' as feature for exons cds on # output 'cds' as feature for exons
start on # output start codons (translation start) start on # output start codons (translation start)
stop on # output stop codons (translation stop) stop on # output stop codons (translation stop)
introns on # output introns introns on # output introns
skipping to change at line 59 skipping to change at line 59
/Constant/ass_end 2 /Constant/ass_end 2
/Constant/dss_start 1 /Constant/dss_start 1
/Constant/dss_end 4 /Constant/dss_end 4
/Constant/init_coding_len 0 /Constant/init_coding_len 0
/Constant/intterm_coding_len 6 /Constant/intterm_coding_len 6
/Constant/tss_upwindow_size 45 /Constant/tss_upwindow_size 45
/Constant/decomp_num_at 1 /Constant/decomp_num_at 1
/Constant/decomp_num_gc 1 /Constant/decomp_num_gc 1
/Constant/gc_range_min 0.32 # This range has an effect only when decomp_num_steps>1. /Constant/gc_range_min 0.32 # This range has an effect only when decomp_num_steps>1.
/Constant/gc_range_max 0.73 # States the minimal and maximal pe rcentage of c or g /Constant/gc_range_max 0.73 # States the minimal and maximal pe rcentage of c or g
/Constant/decomp_num_steps 1 # I recomment keeping this to 1 for most species. /Constant/decomp_num_steps 1 # I recommend keeping this to 1 for most species.
/Constant/min_coding_len 201 # no gene with a coding sequence sh orter than this is predicted /Constant/min_coding_len 201 # no gene with a coding sequence sh orter 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/probNinCoding 0.23 # divide this by .25 to get a malus for making one masked letter part of the coding sequence
/Constant/amberprob 0.243 # Prob(stop codon = tag), if 0 tag is assumed to code for amino acid /Constant/amberprob 0.243 # Prob(stop codon = tag), if 0 tag is assumed to code for amino acid
/Constant/ochreprob 0.374 # Prob(stop codon = taa), if 0 taa is assumed to code for amino acid /Constant/ochreprob 0.374 # Prob(stop codon = taa), if 0 taa is assumed to code for amino acid
/Constant/opalprob 0.383 # Prob(stop codon = tga), if 0 tga is assumed to code for amino acid /Constant/opalprob 0.383 # Prob(stop codon = tga), if 0 tga is assumed to code for amino acid
/Constant/subopt_transcript_threshold 0.7 /Constant/subopt_transcript_threshold 0.7
/Constant/almost_identical_maxdiff 10 /Constant/almost_identical_maxdiff 10
# type of weighing, one of 1 = equalWeights, 2 = gcContentClasses, 3 = multiNor malKernel # type of weighing, one of 1 = equalWeights, 2 = gcContentClasses, 3 = multiNor malKernel
/BaseCount/weighingType 3 /BaseCount/weighingType 3
# file with the weight matrix (only for multiNormalKernel type weighing) # file with the weight matrix (only for multiNormalKernel type weighing)
/BaseCount/weightMatrixFile pisaster_weightmatrix.txt # change this to your sp ecies if at all neccessary /BaseCount/weightMatrixFile pisaster_weightmatrix.txt # change this to your sp ecies if at all necessary
# Properties for IGenicModel # Properties for IGenicModel
# ---------------------------- # ----------------------------
/IGenicModel/verbosity 0 /IGenicModel/verbosity 0
/IGenicModel/infile pisaster_igenic_probs.pbl # change this and the ot her five filenames *_probs.pbl below to your species /IGenicModel/infile pisaster_igenic_probs.pbl # change this and the ot her five filenames *_probs.pbl below to your species
/IGenicModel/outfile pisaster_igenic_probs.pbl /IGenicModel/outfile pisaster_igenic_probs.pbl
/IGenicModel/patpseudocount 5.0 /IGenicModel/patpseudocount 5.0
/IGenicModel/k 4 # order of the Markov chain for content mod el, keep equal to /ExonModel/k /IGenicModel/k 4 # order of the Markov chain for content mod el, keep equal to /ExonModel/k
# Properties for ExonModel # Properties for ExonModel
 End of changes. 3 change blocks. 
3 lines changed or deleted 3 lines changed or added

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