firstSequence=1
lastSequence=2
showSequence=yes
minFrameTestExonLength=0
guaranteeFrameConsistency=yes
startReward=0
stopReward=0
intronScore=0
intronRepeatReward=0
intronRepeatPenalty=0
exonRepeatReward=0
exonRepeatPenalty=0
windowFramePenalty=0
judgeOnlyDP=no
useProteinHomology=yes
numberParses=1
geneSelection=selection
geneDatabase=/data/databases/guigo.seq
selectType=number
geneOrientation=forward
sequenceNumber=1
geneLocus=HS1D3HLH
masking=masking
repeatMask=yes
proteinCDNAMaskFrom=0
proteinCDNAMaskTo=0
computation=computation
generateParse=protein
computeStartStop=yes
spliceSitesScoreWeight=0
proteinHomology=yes
cDNAHomology=no
pairTableMinusOne=no
minusOne=no
spliceStuff=splice
largeStartPairTable=/data/tables/SpliceSites/exon_start_tab.bin
largeStopPairTable=/data/tables/SpliceSites/exon_stop_tab.bin
largeRandPairTable=/data/tables/SpliceSites/rand_tab.bin
smallStartPairTable=/data/tables/SpliceSites/exon_start12_tab.bin
smallStopPairTable=/data/tables/SpliceSites/exon_stop12_tab.bin
smallRandPairTable=/data/tables/SpliceSites/rand_tab.bin
startType=exon
stopType=exon
normalizePairTable=no
displayIntExAve=no
tupleTable=/data2/rosetta/tables/Frametables/6tuples.tupleRankTBL
windowLength=103
scoreMethod=Perk
tupleMethod=Everywhere
exonWeight=1
intronWeight=1
penalty=1
normalMethod=None
normalLengthPower=1
fprobMethod=Normal
proteinStuff=proteins
proteinCodes=/data2/protein.cod
proteinTupIndex=/data2/protein.ind
proteinTupLookup=/data2/protein.loo
proteinTupNum=/data2/protein.tup
proteinSeqIndex=/data2/proteins.ind
proteinSeqLookup=/data2/proteins.loo
proteinTupRank=/data/tables/Frametables/protein.tup.rank
proteinCutoff=8
proteinFrom=1
proteinTo=1
proteinName=ID3_HUMAN
proteinAll=range
proteinPercent=70
cDNAStuff=cdna
cdnaCodes=/data2/cdna.cod
cdnaTupIndex=/data2/cdna.ind
cdnaTupLookup=/data2/cdna.tup.lookup
cdnaTupNum=/data2/cdna.tup
cdnaSeqIndex=/data2/cdna.tup
cdnaSeqLookup=/data2/cdna.tup.lookup
cDNAFrom=1
cDNATo=10
cDNAAll=yes
dpStuff=dp
forceExonPos=0
maxMismatchInExon=100
minimumExonLength=17
minFrametestExonLength=0
minimumIntronLength=70
frameMethod=MinIndex
differentFramePenalty=100
frameTestWeightExon=1
frameTestWeightIntron=1
frameTestLog=no
frameInconsistencyPenalty=1000
bestFrameScoreReward=0
startCutOff=-1000000
stopCutOff=-1000000
majorCheatingStart=no
majorCheatingStop=no
statEvalMethod=Eval
statEvalWindow=0
statEvalWindowWeight=0
displayIntronSignals=no
intronHitsCutoff=5
intronSignalTable=/data/tables/12tup4rega
avgIndicatingExon=0
blastResultsFile=/cpp/main/mouse/col1
mouseGeneDatabase=/data/databases/murinemouse.seq
mouseGeneSequenceNumber=1
generateFoobar=yes
javaOutputFile=/cpp/users/wbeebee/foobar.txt
javaConfigFile=prototype


