eugene.par

#################################################################
###################### GENERAL PARAMETERS #######################
#################################################################
EuGene.version		4.3
EuGene.organism		Arabidopsis
EuGene.mode		Eukaryote  # Eukaryote or Prokaryote
EuGene.sloppy		0
EuGene.VerboseGC	0
EuGene.GCLatency	100000
#
##### Lengths #####
EuGene.InitExDist	init.dist
EuGene.IntrExDist	intr.dist
EuGene.TermExDist	term.dist
EuGene.SnglExDist	sngl.dist
EuGene.IntronDist	intron.dist
EuGene.InterGDist	intergenic.dist
EuGene.5PrimeDist	utr.dist
EuGene.3PrimeDist	utr.dist
EuGene.RnaDist	    rna.dist
EuGene.OverlapDist	overlap.dist
EuGene.UIRDist		uir_prok.dist # only used in Prokaryote mode
#
#
##### Priors #####
EuGene.SplicedStopPen   1e999.0
EuGene.ExonPrior	0.25		# Prior on the initial states
EuGene.IntronPrior	0.15		# Sato et al 1999 / Terryn et al. 1999
EuGene.InterPrior	0.5
EuGene.FivePrimePrior	0.03
EuGene.ThreePrimePrior	0.04
EuGene.RnaPrior         0.03
EuGene.BiCodingPrior    0.00
EuGene.UIRPrior         0.00
#
##### Codon table #####
EuGene.CodonTable	euk.codontable # pro.codontable or euk.codontable
#EuGene.NonCanDon     GC
#EuGene.NonCanAcc     AC
#
#
##### Gff3
Gff3.SoTerms		cfg/sofa.obo
##### Output control ######
Output.RemoveFrags	0
Output.UTRtrim		0
Output.MinCDSLen	60
Output.MinRescueTranscriptLen  100000
Output.truncate		5
Output.initid		0
Output.stepid		1
Output.graph		0		# Don't produce a graphical output
Output.resx		900
Output.resy		400
Output.glen		-1
Output.golap		-1
Output.gfrom		-1
Output.gto		-1
Output.window		48
Output.offset		0
Output.normopt		1
Output.intron		0
Output.format		l
Output.Prefix		./
Output.webdir		LOCAL # or URL: http://www.inra.fr/bia/T/EuGene/
#
##### Alternative splicing predictor control
AltEst.use			0
AltEst.IncompatibilityExonBorderMatchThreshold 100
AltEst.ExonBorderMatchThreshold 0
AltEst.Penalty			1000
AltEst.includedEstFilter		1
AltEst.compatibleEstFilter	0
AltEst.unsplicedEstFilter		0
AltEst.extremeLengthFilter	0
AltEst.maxEstLength		10000
AltEst.minEstLength		100
AltEst.maxIn				10000
AltEst.minIn				40
AltEst.maxEx				10000
AltEst.minEx				3
AltEst.exonucleasicLength	10
AltEst.RepredictMargin		1000
AltEst.altEstDisplay		0
AltEst.strandSpecific	1 
AltEst.verbose			0
#AltEst.reference       /path/of/gff3/reference/annotation        
AltEst.format  		GFF3
#
##### Evaluation mode ######
#Eval.offset   50
Eval.ignoreNpcRNA 1      # Put 1 to ignore the npcRNA for the fitness computing.
Fitness.wsng  1
Fitness.wsne  1
Fitness.wsnn  0
Fitness.wspg  1
Fitness.wspe  1
Fitness.wspn  0
#
##### Operon parameter ######
Operon.maxDistance 10
Operon.initid      0
#
#######################################################################
################### SIGNAL SENSORS PARAMETERS####################
#################################################################
#
##### EuStop parameters #####
EuStop.stopP*           4.155
#
##### FrameShift parameters #####
FrameShift.Ins*		1e999.0
FrameShift.Del*		1e999.0
#
##### RibosomalFrameShift sensor (uniform penalties) #####
RibosomalFrameShift.type[0]	deletion3   # Possible types: deletion1 deletion2 deletion3 insertion1 insertion2 insertion3
RibosomalFrameShift.pat[0]		AAAAAAC	
RibosomalFrameShift.newStatePos[0] 4	# Position of the new state in the pattern
RibosomalFrameShift.patP*[0]	-10
RibosomalFrameShift.patPNo*[0]	0
RibosomalFrameShift.requiredEstSupport[0]	1 # 1 if an EST support is required
#
##### GeneSplicer parameters #####
GSplicer.coefAcc*	1
GSplicer.penAcc*	0
GSplicer.coefDon*	1
GSplicer.penDon* 	0
#GSplicer.format      GFF3
#
##### PepSignal #####
PepSignal.startP*	1
PepSignal.startB*	0
#PepSignal.format     GFF3
#
##### SpliceMachine parameters #####
SMachine.cmd		"splicemachine.pl "
SMachine.isScaled	1
SMachine.accP*		0.102032725565
SMachine.accB*		5.585
SMachine.donP*		0.020202707318
SMachine.donB*		27.670
SMachine.startP*	0.052
SMachine.startB*	0.308
SMachine.tSpliceB*	0.0
#SMachine.format      GFF3
#
# NetGene2 parameters #####
NG2.accP*[0]	0.903
NG2.accB*[0]	5.585
NG2.donP*[0]	0.980
NG2.donB*[0]	27.670
NG2.accP*[1]	0.903
NG2.accB*[1]	5.585
NG2.donP*[1]	0.980
NG2.donB*[1]	27.670
#NG2.format           GFF3
#
##### NetStart parameters #####
NStart.startP*		0.052
NStart.startB*		0.308
#
##### ProStart parameters #####
#
ProStart.matchlen	14
ProStart.matchoffset	3
ProStart.RBSPattern attcctcca # E coli (16S genetics/ Steitz J.A.)
ProStart.alpha*	0.4
ProStart.beta*	6.0
ProStart.stackFile stack.dat
ProStart.loopFile loop.dat
#
##### PatConst sensor (uniform penalties) #####
PatConst.type[0]	donor   # Possible types : start insertion deletion
PatConst.pat[0]		GC	#  transstart transstop stop acceptor donor
PatConst.newStatePos[0] 1       # Position of the new state in the pattern
PatConst.patP*[0]	-10
PatConst.patPNo*[0]	0
#
#PatConst.type[1]	acceptor
#PatConst.pat[1]		AG
#PatConst.newStatePos[1] 3
#PatConst.patP*[1]	1e-9
#PatConst.patPNo*[1]	0
#
#PatConst.type[2]	start
#PatConst.pat[2]		ATG
#PatConst.newStatePos[2] 1
#PatConst.patP*[2]	2.897949
#PatConst.patPNo*[2]	0
#
#
#### SignalWAM instances #####
#
SignalWAM.type[0]            acceptor   # allowed values: start, donor, acceptor 
SignalWAM.species[0]         plant
SignalWAM.scaleCoef*[0]      1.887040
SignalWAM.scalePenalty*[0]   -5.676197
SignalWAM.scoringMode[0]     0
SignalWAM.spliceNonCan[0]    0
#
SignalWAM.type[1]            donor      # allowed values: start, donor, acceptor
SignalWAM.species[1]         plant
SignalWAM.scaleCoef*[1]      1.887040
SignalWAM.scalePenalty*[1]  -5.676197
SignalWAM.spliceNonCan[1]    0
#
#
##### SplicePredictor parameters #####
SPred.accP*[0]	0.987
SPred.accB*[0]	3.850
SPred.donP*[0]	0.929
SPred.donB*[0]	10.800
SPred.accP*[1]	0.987
SPred.accB*[1]	3.850
SPred.donP*[1]	0.929
SPred.donB*[1]	10.800
#SPred.format GFF3
#
##### Transcript parameters #####
Transcript.Start*	4.155
Transcript.Stop*	4.155
Transcript.StartNpc* 30
Transcript.StopNpc* 30
Transcript.AffectedStrand  0 #  0 (both) or -1 (strand minus) or 1 (strand plus)
#
#################################################################
################# CONTENT SENSORS PARAMETERS ####################
#################################################################
#
##### Proteic similarity sensor parameters #####
BlastX.PostProcess 0    # 0 1 OR 2
BlastX.PPNumber	   5    # For PostProcess = "2"
BlastX.levels	  012
BlastX.activegaps NONE
BlastX.level0*	0.2
BlastX.level1*	0.05
BlastX.level2*	0.0
BlastX.level3*	0.0
BlastX.level4*	0.0
BlastX.level5*	0.0
BlastX.level6*	0.0
BlastX.level7*	0.0
BlastX.level8*	0.0
BlastX.level9*	0.0
BlastX.blastxM*	10	
BlastX.minIn 50
#BlastX.format   GFF3
#
##### Est sensor parameters #####
Est.PostProcess[0]	0     # 0 1 OR 2
Est.PPNumber[0]	5     # For PostProcess = "2"
Est.estP*[0]	-0.4
#Est.estP*[0]	-1e4  # forces EuGene to match with est
Est.estM[0]	6
Est.utrP*[0]	0.35
Est.utrM[0]	5
Est.CdsBoost*[0] 0.0
Est.SpliceBoost*[0] 0.0
Est.SpliceNonCanP[0] 1.0
Est.SpliceStartP[0] 100.0
Est.StrongDonor[0] 0.95
Est.MinDangling[0] 10
Est.MaxIntron[0]   15000
Est.MaxInternalIntron[0]   15000
Est.mRNAOnly[0] 1   # 1 if the file contains only hits of mrna, 0 if the file contains hits of mrna or ncrna (in this case, ncrna tracks are not penalized)
Est.FileExtension[0]	.est
#Est.format[0]    GFF3
#
Est.PostProcess[1]	0     # 0 1 OR 2
Est.PPNumber[1]	5     # For PostProcess = "2"
Est.estP*[1]	-0.4
#Est.estP*[1]	-1e4  # forces EuGene to match with est
Est.estM[1]	6
Est.utrP*[1]	0.35
Est.utrM[1]	5
Est.CdsBoost*[1] 0.0
Est.SpliceBoost*[1] 0.0
Est.SpliceNonCanP[1] 1.0
Est.SpliceStartP[1] 100.0
Est.StrongDonor[1] 0.95
Est.MinDangling[1] 10
Est.MaxIntron[1]   15000
Est.MaxInternalIntron[1]   15000
Est.mRNAOnly[1] 1   # 1 if the file contains only hits of mrna, 0 if the file contains hits of mrna or ncrna (in this case, ncrna tracks are not penalized)
Est.FileExtension[1]	.est2
#Est.format[1]    GFF3
#
##### Homology Sensor parameters #####
Homology.TblastxP*[0]	0
Homology.TblastxB*[0] 	0.0595
Homology.protmatname[0]    BLOSUM80
Homology.MaxHitLen[0]  15000
#Homology.format[0]              GFF3
Homology.FileExtension[0]	.tblastx
Homology.TblastxP*[1]	0
Homology.TblastxB*[1] 	0.0595
Homology.protmatname[1]    BLOSUM80
Homology.MaxHitLen[1]  15000
#Homology.format[1]        GFF3
Homology.FileExtension[1]	.tblastx2
#
##### State penalties per position #####
MarkovConst.minGC[0]	-1
MarkovConst.maxGC[0]	100
MarkovConst.Coding*	1.0
MarkovConst.Intron*	1.0
MarkovConst.IntronUTR*	0.98
MarkovConst.UTR5*	0.99
MarkovConst.UTR3*	0.99
MarkovConst.UIR*	0.99
MarkovConst.RNA*	1.0
MarkovConst.Inter*	1.0
MarkovConst.affectedStrand  0      # 0 (both) or -1 (strand minus) or 1 (strand plus)
#
##### Interpolated Markov Models parameters #####
MarkovIMM.matname[0]	Ara2UTR.mat
MarkovIMM.minGC[0]	0
MarkovIMM.maxGC[0]	100
MarkovIMM.IntergenicModel[0]	2
MarkovIMM.npcRNAModel[0] gc
MarkovIMM.maxOrder[0]	8
MarkovIMM.CodingPot[0]  100
#MarkovIMM.matname[1]	Ara2UTR.mat
#MarkovIMM.minGC[1]	50
#MarkovIMM.maxGC[1]	100
#MarkovIMM.IntergenicModel[1]	2
#MarkovIMM.npcRNAModel[1] gc
#MarkovIMM.maxOrder[1]	8
#MarkovIMM.CodingPot[1]  100
#
##### Markov proteic model parameters #####
MarkovProt.matname[0]	SwP41.noFragm.mininfo1.order2.bin
MarkovProt.minGC[0]	0
MarkovProt.maxGC[0]	100
MarkovProt.maxorder     2
MarkovProt.order        2
#
##### Repeat sensor parameters #####
Repeat.UTRPenalty*	0.0
Repeat.IntronPenalty*	0.1
Repeat.ExonPenalty*	1.0
#Repeat.format        GFF3
##### NStretch sensor parameters #####
NStretch.stretchPenalty 1.0
NStretch.maxLengthWithoutPenalty      5000
#
##### NcRNA sensor parameters ####
NcRNA.FileExtension[0]  ncrna
NcRNA.NpcRna*[0] 1 
NcRNA.TStartNpc*[0] 1
NcRNA.TStopNpc*[0] 1	
NcRNA.format[0]        GFF3 # Mandatory
#
NcRNA.FileExtension[1]  trna
NcRNA.NpcRna*[1] 1 
NcRNA.TStartNpc*[1] 1
NcRNA.TStopNpc*[1] 1	
NcRNA.format[1]        GFF3 # Mandatory
#
#################################################################
############## SIGNAL/CONTENT SENSORS PARAMETERS ################
#################################################################
#
##### Sensors AnnotaStruct #####
AnnotaStruct.FileExtension[0]      genefinder1
AnnotaStruct.TranscriptFeature[0]  transcript
AnnotaStruct.Start*[0]             0.1    # i: inline score (GFF3 format only)
AnnotaStruct.StartType[0]          p      # p: probability  s: score  
AnnotaStruct.Stop*[0] 0.2
AnnotaStruct.StopType[0] p
AnnotaStruct.Acc*[0] 0.3
AnnotaStruct.AccType[0] p
AnnotaStruct.Don*[0] 0.4
AnnotaStruct.DonType[0] p
AnnotaStruct.TrStart*[0] 0.5
AnnotaStruct.TrStartType[0] p
AnnotaStruct.TrStop*[0] 0.6
AnnotaStruct.TrStopType[0] p
AnnotaStruct.TrStartNpc*[0] 0.5
AnnotaStruct.TrStartNpcType[0] p
AnnotaStruct.TrStopNpc*[0] 0.5
AnnotaStruct.TrStopNpcType[0] p
AnnotaStruct.Exon*[0] 2
AnnotaStruct.Intron*[0] 3
AnnotaStruct.CDS*[0] 4
AnnotaStruct.npcRNA*[0]  2
AnnotaStruct.Intergenic*[0]  0
AnnotaStruct.format[0]             GFF3
#
AnnotaStruct.FileExtension[1]      genefinder2
AnnotaStruct.TranscriptFeature[1]  transcript
AnnotaStruct.Start*[1]             1    # i: inline score (GFF3 format only)
AnnotaStruct.StartType[1]          s      # p: probability  s: score  
AnnotaStruct.Stop*[1] 2
AnnotaStruct.StopType[1] s
AnnotaStruct.Acc*[1] 0.0
AnnotaStruct.AccType[1] s
AnnotaStruct.Don*[1] 0.0
AnnotaStruct.DonType[1] s
AnnotaStruct.TrStart*[1] 0.0
AnnotaStruct.TrStartType[1] s
AnnotaStruct.TrStop*[1] 0.0
AnnotaStruct.TrStopType[1] s
AnnotaStruct.TrStartNpc*[1] 0
AnnotaStruct.TrStartNpcType[1] s
AnnotaStruct.TrStopNpc*[1] 0
AnnotaStruct.TrStopNpcType[1] s
AnnotaStruct.Exon*[1] 2
AnnotaStruct.Intron*[1] 3
AnnotaStruct.CDS*[1] 4
AnnotaStruct.npcRNA*[1]  2
AnnotaStruct.Intergenic*[1]  0
#AnnotaStruct.format[1]             GFF3
#
##### IfElse #####
IfElse.SensorIf		NG2
IfElse.SensorElse	SPred
#
##### Riken sensor parameters #####
Riken.StrandRespect			0
Riken.Min_est_diff			100
Riken.Max_overlap			60
Riken.Max_riken_length			60000
Riken.Max_riken_est_length		3000
Riken.Min_riken_length			120 
Riken.Min_riken_est_length		10
Riken.RAFLPenalty*			-120.0
#Riken.format                  		GFF3
#
#################################################################
################## OTHERS SENSORS PARAMETERS ####################
#################################################################
#
##### Sensor GCPlot #####
GCPlot.Color	5
GCPlot.Zoom	2.0
GCPlot.Zoom3	1.0
GCPlot.Up	GC
GCPlot.Over	ATGC
GCPlot.Smooth	100
#
##### GFF sensor parameters #####
GFF.PostProcess		1
#
##### Sensor Plotter
Plotter.GC	 1   # 0 -> no plot  -  1 -> plot 
Plotter.GC3	 1   #
Plotter.A|T/A+T	 0   # T/A+T -> IntronF - A/A+T -> IntronR
#
##### Sensor Tester #####
Tester.Make		SPSN	# SPSN, TEST
Tester.Sensor		EuStop
Tester.Sensor.Instance	0
Tester.SPSN.MinNumbers	100     # greater than 0
Tester.SPSN.Eval        STOP    # START, STOP, SPLICE
#
#################################################################
################# SENSORS CONFIGURATION PARAMETERS ##############
#################################################################
#
##### Sensors activation #####
# SIGNAL SENSORS
Sensor.EuStop.use	1
Sensor.FrameShift.use	0
Sensor.GSplicer.use	0
Sensor.SMachine.use	0
Sensor.NG2.use		0
Sensor.NStart.use	1
Sensor.PatConst.use	0
Sensor.PepSignal.use	0
Sensor.RibosomalFrameShift.use     0
Sensor.SignalWAM.use    0
Sensor.SPred.use	0
Sensor.Transcript.use	1
Sensor.ProStart.use	0
#
# CONTENT SENSORS
Sensor.BlastX.use	0
Sensor.Est.use		0	
Sensor.Homology.use	0	
Sensor.MarkovConst.use	1
Sensor.MarkovIMM.use	1
#Sensor.MarkovIMM.use	2
Sensor.MarkovProt.use	0
Sensor.Repeat.use	0
Sensor.NStretch.use     0
Sensor.NcRNA.use        0
#
# SIGNAL/CONTENT SENSORS
Sensor.AnnotaStruct.use 0
Sensor.IfElse.use	1
Sensor.Riken.use	0
Sensor.QualData.use     0
#
# OTHERS SENSORS
Sensor.GCPlot.use	0
Sensor.GFF.use		0
Sensor.Plotter.use	0
Sensor.Tester.use	0
#
Qual.factor*		5.0
#
##### Sensor priorities	 #####
#  the lower the priority, the first loaded sensor
# SIGNAL SENSORS
Sensor.EuStop 		10
Sensor.FrameShift 	10
Sensor.GSplicer 	10
Sensor.NG2 		10
Sensor.NStart 		10
Sensor.PatConst 	10
Sensor.PepSignal 	10
Sensor.RibosomalFrameShift 30
Sensor.SMachine 	10
Sensor.SignalWAM    10
Sensor.SPred 		10
Sensor.Transcript 	10
Sensor.ProStart		10
#
# CONTENT SENSORS
Sensor.BlastX 		10
Sensor.Est 		20
Sensor.Homology   	10
Sensor.MarkovConst 	10
Sensor.MarkovIMM 	1
Sensor.MarkovProt 	1
Sensor.Repeat 		10
Sensor.NStretch         1
Sensor.NcRNA            1
#
# SIGNAL/CONTENT SENSORS
Sensor.AnnotaStruct     1
Sensor.IfElse 		10
Sensor.Riken 		10
#
# OTHERS SENSORS
Sensor.GCPlot 		1
Sensor.GFF 		10
Sensor.Plotter 		1
Sensor.Tester 		1
#
#
#################################################################
################### OPTIMIZATION PARAMETERS #####################
#################################################################
ParaOptimization.Use 0
ParaOptimization.Regularizer	0.0
ParaOptimization.TrueCoordFile ---
ParaOptimization. EvalPredDir ../Procedures/Eval
ParaOptimization.Algorithm GENETIC+LINESEARCH
ParaOptimization.Test 0
ParaOptimization.Trace 1
#
ParaOptimization.NbCluster 3
ParaOptimization.Cluster[0] LINKED
ParaOptimization.Cluster[1] IDENTICAL
ParaOptimization.Cluster[2] IDENTICAL
#
ParaOptimization.NbParameter 5
#
ParaOptimization.Para.Name[0] para1*
ParaOptimization.Para.Max[0] 1
ParaOptimization.Para.Min[0] 0
ParaOptimization.Para.Cluster[0] 0
#
ParaOptimization.Para.Name[1] para2*
ParaOptimization.Para.Max[1] 1
ParaOptimization.Para.Min[1] 0
ParaOptimization.Para.Cluster[1] 0
#
ParaOptimization.Para.Name[2] para3*
ParaOptimization.Para.Max[2] 1
ParaOptimization.Para.Min[2] 0
ParaOptimization.Para.Cluster[2] 1
#
ParaOptimization.Para.Name[3] para4*
ParaOptimization.Para.Max[3] 1
ParaOptimization.Para.Min[3] 0
ParaOptimization.Para.Cluster[3] 1
#
ParaOptimization.Para.Name[4] para5*
ParaOptimization.Para.Max[4] 1
ParaOptimization.Para.Min[4] 0
ParaOptimization.Para.Cluster[4] 2
#
################## Genetic ######################################
Genetic.NbRun 2
Genetic.NbGeneration 2
Genetic.NbElement 10
Genetic.CrossOverProbability 0.6
Genetic.MutationProbability 0.2
Genetic.SelectionType 1
#				  1:stochastic remainder without replacement
Genetic.ScalingType 1
#				  1: Sigma Truncation scaling 
#				  2: Power Law scaling
Genetic.Sharing 0.9
#				  1: sharing, looking for clusters which best 
#				     elt fitness is at least n% of the overall 
#	                             best element of the population
Genetic.Clustering 1
Genetic.Elitism 0.9
#				  n: elitism; keeps the best elt if no sharing,
#	                             and keeps the best elt of each cluster 
#				     which best_elt fitness is at
#	                             least n% of the overallbest elt if sharing
Genetic.SA.Mutation 0
Genetic.SA.CrossOver 0
Genetic.Seed 4
#
#
######### LINESEARCH ###########################################
LineSearch.NbMaxCycle 10
LineSearch.NbMinCycle 2
LineSearch.NbMaxStab 2
LineSearch.DivInter 4
LineSearch.Alpha 0.6
LineSearch.EvolutionMini 0.001
LineSearch.Seed 1
#
LineSearch.Para.Step[0] 0.01
LineSearch.Para.Init[0] 0.5
LineSearch.Para.MaxInit[0] 1
LineSearch.Para.MinInit[0] 0
#
LineSearch.Para.Step[1] 0.01
LineSearch.Para.Init[1] 0.5
LineSearch.Para.MaxInit[1] 1
LineSearch.Para.MinInit[1] 0
#
LineSearch.Para.Step[2] 0.01
LineSearch.Para.Init[2] 0.5
LineSearch.Para.MaxInit[2] 1
LineSearch.Para.MinInit[2] 0
#
LineSearch.Para.Step[3] 0.01
LineSearch.Para.Init[3] 0.5
LineSearch.Para.MaxInit[3] 1
LineSearch.Para.MinInit[3] 0
#
LineSearch.Para.Step[4]	0.01
LineSearch.Para.Init[4] 0.5
LineSearch.Para.MaxInit[4] 1
LineSearch.Para.MinInit[4] 0