"Fossies" - the Fresh Open Source Software Archive  

Source code changes of the file "config/species/s_aureus/s_aureus_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.

s_aureus_parameters.cfg  (augustus-3.3.2):s_aureus_parameters.cfg  (augustus-3.3.3)
skipping to change at line 12 skipping to change at line 12
# s_aureus parameters. (Staphylococcus aureus) # s_aureus parameters. (Staphylococcus aureus)
# #
# date : 21.8.2014 # date : 21.8.2014
# #
# #
# Properties for augustus # Properties for augustus
#------------------------------------ #------------------------------------
genemodel bacterium # no introns, overlapping genes, etc genemodel bacterium # no introns, overlapping genes, etc
translation_table 11 # prokaryotic genetic code translation_table 11 # prokaryotic genetic code
/augustus/verbosity 3 # 0-3, 0: only print the neccessary /augustus/verbosity 3 # 0-3, 0: only print the necessary
maxDNAPieceSize 2000000 # maximum segment that is predicted in one piece maxDNAPieceSize 2000000 # maximum segment that is predicted in one piece
stopCodonExcludedFromCDS false # make this 'true' if the CDS includes the stop c odon (training and prediction) stopCodonExcludedFromCDS false # make this 'true' if the CDS includes the stop c odon (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 61 skipping to change at line 61
/Constant/ass_end 2 /Constant/ass_end 2
/Constant/dss_start 3 /Constant/dss_start 3
/Constant/dss_end 3 /Constant/dss_end 3
/Constant/init_coding_len 4 /Constant/init_coding_len 4
/Constant/intterm_coding_len 5 /Constant/intterm_coding_len 5
/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 0.22 # This range has an effect only when decomp_num_steps>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 pe rcentage of c or g /Constant/gc_range_max 0.42 # States the minimal and maximal pe rcentage of c or g
/Constant/decomp_num_steps 2 # I recomment keeping this to 1 for most species. /Constant/decomp_num_steps 2 # I recommend keeping this to 1 for most species.
/Constant/min_coding_len 61 # no gene with a coding sequence sh orter than this is predicted /Constant/min_coding_len 61 # 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 0.067 # Prob(stop codon = tag), if 0 tag is assumed to code for amino acid /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/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/opalprob 0.255 # 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 s_aureus_weightmatrix.txt # change this to your sp ecies if at all neccessary /BaseCount/weightMatrixFile s_aureus_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 s_aureus_igenic_probs.pbl # change this and the ot her five filenames *_probs.pbl below to your species /IGenicModel/infile s_aureus_igenic_probs.pbl # change this and the ot her five filenames *_probs.pbl below to your species
/IGenicModel/outfile s_aureus_igenic_probs.pbl /IGenicModel/outfile s_aureus_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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