AlignmentMatrix <- function(LTRpred.seqs){
# LTRpred predicted LTR transposon sequences
#pred.seqs <- read.seqs(LTRpred.seqs)
GlobalAlignmentScoreMatrix <- matrix(NA_real_, ncol = length(LTRpred.seqs), nrow = length(LTRpred.seqs))
for (i in 1:length(LTRpred.seqs)){
for(j in 1:length(LTRpred.seqs)){
if (is.na(GlobalAlignmentScoreMatrix[i,j])){
GlobalAlignmentScoreMatrix[i,j] <- NW.Align(LTRpred.seqs[i],LTRpred.seqs[j])@score
GlobalAlignmentScoreMatrix[j,i] <- GlobalAlignmentScoreMatrix[i,j]
}
}
}
# colnames(GlobalAlignmentScoreMatrix) <- names(LTRpred.seqs)
# rownames(GlobalAlignmentScoreMatrix) <- names(LTRpred.seqs)
return (GlobalAlignmentScoreMatrix)
}
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