#' Finds the optimal global nucleotide sequence aligment with Needleman-Wunsch algorithm with BLOSUM50 as score matrix.
#'
#' @param sequence1 First vector with characters indicating some protein sequence.
#' @param sequence2 Second vector with characters indicating some protein sequence.
#' @param gapPenalty A number indicating the gap penalty value.
#' @param blosumName Name of the BLOSUM matrix.
#' @return List containing the score, the resulting aligned sequences and the matrix of aligment.
#' @examples
#' globalAligmentProteinSequence(c("P","A","W","H","E","A","E"), c("H","E","A","G","A","W","G","H","E","E"), 8, "BLOSUM50")
globalAligmentProteinSequence <- function(sequence1, sequence2, gapPenalty, blosumName){
if(exists(blosumName) == FALSE)
return("BLOSUM matrix with that name isn't available")
BLOSUM <- get(blosumName)
if(gapPenalty > 0)
d = gapPenalty * -1
else
d = gapPenalty
matrix <- matrix(data = NA, nrow = length(sequence1) + 1, ncol = length(sequence2) + 1)
dimnames(matrix) <- list(c("-", sequence1), c("-", sequence2))
matrix[1,1] = 0 #prviot element e nula
# popolnuvanje na prva kolona
for(i in 2:nrow(matrix)){
matrix[i,1] = (i - 1) * d
}
# popolnuvanje na prv red
for(j in 2:ncol(matrix)){
matrix[1,j] = (j - 1) * d
}
# presmetka na matricata
for(i in 2:nrow(matrix)){
for(j in 2:ncol(matrix)){
rowname <- rownames(matrix)[i]
colname <- colnames(matrix)[j]
match <- matrix[i-1,j-1] + BLOSUM[rowname, colname]
delete <- matrix[i-1,j] + d
insert <- matrix[i,j-1] + d
matrix[i,j] <- max(match, insert, delete)
}
}
finalScore <- matrix[nrow(matrix),ncol(matrix)]
# back track
newSequence1 <- ""
newSequence2 <- ""
i <- nrow(matrix)
j <- ncol(matrix)
while(i > 1 && j > 1){
score <- matrix[i,j]
scoreDiag <- matrix[i-1,j-1]
scoreLeft <- matrix[i,j-1]
scoreUp <- matrix[i-1,j]
rowname <- rownames(matrix)[i]
colname <- colnames(matrix)[j]
if(score == scoreUp + d){
newSequence1 <- paste(rowname, newSequence1, sep = "")
newSequence2 <- paste("-", newSequence2, sep = "")
i <- i - 1
}
else if(score == scoreLeft + d){
newSequence1 <- paste("-", newSequence1, sep = "")
newSequence2 <- paste(colname, newSequence2, sep = "")
j <- j - 1
}
else{
newSequence1 <- paste(rowname, newSequence1, sep = "")
newSequence2 <- paste(colname, newSequence2, sep = "")
i <- i - 1
j <- j - 1
}
}
while(i > 1){
rowname <- rownames(matrix)[i]
score <- matrix[i,j]
newSequence1 <- paste(rowname, newSequence1, sep = "")
newSequence2 <- paste("-", newSequence2, sep = "")
i <- i - 1
}
while(j > 1){
colname <- colnames(matrix)[j]
score <- matrix[i,j]
newSequence1 <- paste("-", newSequence1, sep = "")
newSequence2 <- paste(colname, newSequence2, sep = "")
j <- j - 1
}
solution = list(score = finalScore, sequence1 = newSequence1, sequence2 = newSequence2, matrix = matrix)
return(solution)
}
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