Biostrings (version 2.40.2)

needwunsQS: (Deprecated) Needleman-Wunsch Global Alignment

Description

Simple gap implementation of Needleman-Wunsch global alignment algorithm.

Usage

needwunsQS(s1, s2, substmat, gappen = 8)

Arguments

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.

Value

An instance of class "PairwiseAlignments".

Details

Follows specification of Durbin, Eddy, Krogh, Mitchison (1998). This function has been deprecated and is being replaced by pairwiseAlignment.

References

R. Durbin, S. Eddy, A. Krogh, G. Mitchison, Biological Sequence Analysis, Cambridge UP 1998, sec 2.3.

See Also

pairwiseAlignment, PairwiseAlignments-class, substitution.matrices

Examples

## 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")
# ## End(Not run)