Question: traceback algorithm global alignment in R code

0

gizemtatar •

**0**wrote:My needleman-wunsch global alignment scoring matrix :

G C A T G C U

0 -1 -2 -3 -4 -5 -6 -7

G -1 1 0 -1 -2 -3 -4 -5

A -2 0 0 1 0 -1 -2 -3

T -3 -1 -1 0 2 1 0 -1

T -4 -2 -2 -1 1 1 0 -1

A -5 -3 -3 -1 0 0 0 -1

C -6 -4 -2 -2 -1 -1 1 0

A -7 -5 -3 -1 -2 -2 0 0

I want traceback algorithm and find best alignment sequence.

I try for this code.

Astring <- strsplit(A, "")[[1]] Bstring <- strsplit(B, "")[[1]] n=length(Astring) #seq1 m=length(Bstring) #seq2 s=matrix(data = 0, nrow = m, ncol =n, dimnames = list(Bstring,Astring)) for (i in seq_len(m)) for (j in seq_len(n)) { if (Astring[j]==Bstring[i]) s[i,j]<- 1 else s[i,j]<- -1 } fmatrix = matrix(0, nrow = (nchar(A)+1) , ncol = nchar(B)+1) d = -1 #this is gap penalty for(i in 0 : nchar(B)){ fmatrix[i+1,1] = d * i #populates initial row with gap penalty } for(j in 0 : nchar(A)){ fmatrix[1,j+1] = d * j } for(i in 1 : nchar(B)){ for(j in 1 : nchar(A)) { #get me sccore for the pair of aa or nt match = fmatrix[i,j] + s[i,j] delete = fmatrix[i,j+1] + d insert = fmatrix[i+1,j] + d fmatrix[i+1,j+1] = max(match,delete,insert) } } colnames(fmatrix) = strsplit( paste(" " , A, sep=""), "")[[1]]; rownames(fmatrix) = strsplit( paste(" " , B, sep=""), "")[[1]]; #return(fmatrix) AlignmentA = "" AlignmentB = "" i = nchar(B) +1 j = nchar(A) +1 maxscore=numeric(length=0) while(i > 1 && j > 1) { CurrentScore= fmatrix[i,j] ScoreDiag= fmatrix[i-1,j-1] ScoreLeft=fmatrix[i,j-1] ScoreUp=fmatrix[i-1,j] maxscore= max(CurrentScore,ScoreDiag,ScoreLeft,ScoreUp) if( CurrentScore <= ScoreDiag ) { AlignmentA=paste(substr(A,j-1,j-1),AlignmentA, sep="") AlignmentB=paste(substr(B,i-1,i-1),AlignmentB, sep="") j=j-1 i=i-1 } else if (ScoreLeft >= CurrentScore) { AlignmentA=paste(substr(A,j-1,j-1),AlignmentA, sep="") AlignmentB=paste("-",AlignmentB, sep="") j=j-1 } else if (CurrentScore>=ScoreUp+d) { AlignmentA=paste("-",AlignmentA, sep="") AlignmentB=paste(substr(B,i-1,i-1),AlignmentB, sep="") i=i-1 } ans <- matrix(c(al1=paste(AlignmentA, collapse=""), al2=paste(AlignmentB, collapse=""))) print(ans)

But I don't find best alignment. The best alignments :

GCATG-CU GCA-TGCU GCAT-GCU G-ATTACA G-ATTACA G-ATTACA

Can you help this topic please?

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modified 4 months ago
by
parkkh1188 •

**0**• written 4.7 years ago by gizemtatar •**0**
Why reinvent the wheel when

`pairwiseAlignment()`

is a well tested function from`Biostrings`

that does all of this for you anyway?25kI need manual R code.

0For an assignment?

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