(Deprecated) Needleman-Wunsch Global Alignment
Simple gap implementation of Needleman-Wunsch global alignment algorithm.
needwunsQS(s1, s2, substmat, gappen = 8)
s1, s2 |
an R character vector of length 1 or an XString object. |
substmat |
matrix of alignment score values. |
gappen |
penalty for introducing a gap in the alignment. |
Follows specification of Durbin, Eddy, Krogh, Mitchison (1998).
This function has been deprecated and is being replaced by
pairwiseAlignment.
An instance of class "PairwiseAlignments".
Vince Carey (stvjc@channing.harvard.edu) (original author) and H. Pagès (current maintainer).
R. Durbin, S. Eddy, A. Krogh, G. Mitchison, Biological Sequence Analysis, Cambridge UP 1998, sec 2.3.
## Not run:
## This function has been deprecated
## Use 'pairwiseAlignment' instead.
## nucleotide alignment
mat <- matrix(-5L, nrow = 4, ncol = 4)
for (i in seq_len(4)) mat[i, i] <- 0L
rownames(mat) <- colnames(mat) <- DNA_ALPHABET[1:4]
s1 <- DNAString(paste(sample(DNA_ALPHABET[1:4], 1000, replace=TRUE), collapse=""))
s2 <- DNAString(paste(sample(DNA_ALPHABET[1:4], 1000, replace=TRUE), collapse=""))
nw0 <- needwunsQS(s1, s2, mat, gappen = 0)
nw1 <- needwunsQS(s1, s2, mat, gappen = 1)
nw5 <- needwunsQS(s1, s2, mat, gappen = 5)
## amino acid alignment
needwunsQS("PAWHEAE", "HEAGAWGHEE", substmat = "BLOSUM50")
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