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Source code changes of the file "config/species/aspergillus_nidulans/aspergillus_nidulans_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.

aspergillus_nidulans_parameters.cfg  (augustus-3.3.2):aspergillus_nidulans_parameters.cfg  (augustus-3.3.3)
# #
# aspergillus_nidulans parameters. # aspergillus_nidulans parameters.
# #
# date : 19.12.2006 # date : 19.12.2006
# #
# #
# 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 200000 # maximum segment that is predicted in one piece maxDNAPieceSize 200000 # maximum segment that is predicted in one piece
stopCodonExcludedFromCDS true # make this 'true' if the CDS includes the stop co don (training and prediction) stopCodonExcludedFromCDS true # make this 'true' if the CDS includes the stop co don (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 70 skipping to change at line 70
/Constant/probNinCoding 0.23 /Constant/probNinCoding 0.23
/Constant/amberprob 0.33 # Prob(stop codon = tag), if 0 tag is assumed to code for amino acid /Constant/amberprob 0.33 # Prob(stop codon = tag), if 0 tag is assumed to code for amino acid
/Constant/ochreprob 0.33 # Prob(stop codon = taa), if 0 taa is assumed to code for amino acid /Constant/ochreprob 0.33 # Prob(stop codon = taa), if 0 taa is assumed to code for amino acid
/Constant/opalprob 0.34 # Prob(stop codon = tga), if 0 tga is assumed to code for amino acid /Constant/opalprob 0.34 # 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 aspergillus_nidulans_weightmatrix.txt # change thi s to your species if at all neccessary /BaseCount/weightMatrixFile aspergillus_nidulans_weightmatrix.txt # change thi s to your species if at all necessary
# Properties for IGenicModel # Properties for IGenicModel
# ---------------------------- # ----------------------------
/IGenicModel/verbosity 0 /IGenicModel/verbosity 0
/IGenicModel/infile aspergillus_nidulans_igenic_probs.pbl # change thi s and the other five filenames *_probs.pbl below to your species /IGenicModel/infile aspergillus_nidulans_igenic_probs.pbl # change thi s and the other five filenames *_probs.pbl below to your species
/IGenicModel/outfile aspergillus_nidulans_igenic_probs.pbl /IGenicModel/outfile aspergillus_nidulans_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. 2 change blocks. 
2 lines changed or deleted 2 lines changed or added

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