(Defunct) Needleman-Wunsch Global Alignment

Description

Simple gap implementation of Needleman-Wunsch global alignment algorithm.

Usage

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

Arguments

Details

Follows specification of Durbin, Eddy, Krogh, Mitchison (1998). This function is now defunct. Please use pairwiseAlignment from the pwalign instead.

Value

An instance of class "PairwiseAlignments".

Author(s)

Vince Carey (stvjc@channing.harvard.edu) (original author) and H. Pagès (current maintainer).

References

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

See Also

pairwiseAlignment and PairwiseAlignments-class in the pwalign package, substitution_matrices

Examples

## Not run: 
  ## This function is now defunct.
  ## Please use pairwiseAlignment() from the pwalign package 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)