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| hmm=initHMM(c("P","N"),names(d[,1]),transProbs=matrix(c(0.999,0.000008,
0.001,0.999992),2),emissionProbs=matrix(rbind(d[,1],d[,2]),2))
A=read.fasta("concat_encodeENm001.fa")
AA=paste(A[1:(length(A)-1)],A[2:length(A)],sep="")
res1=viterbi(hmm,AA)
lim1=which(res1[2:length(res1)]!=res1[1:(length(res1)-1)])
lim1
fin1=which(res1[2:length(res1)]=="N" & res1[1:(length(res1)-1)]=="P")
deb1=which(res1[2:length(res1)]=="P" & res1[1:(length(res1)-1)]=="N")
if (length(deb1)<length(fin1)){fin1=fin1[2:length(fin1)]}
rect(deb1,0.9,fin1,1.1,col="blue") |
