needwunsQS: (Deprecated) Needleman-Wunsch Global Alignment

In anandhupresannan/biostrings: Efficient manipulation of biological strings

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.

Details

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

Value

An instance of class "PairwiseAlignments".

Author(s)

Vince Carey ([e-mail]) (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, 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)

anandhupresannan/biostrings documentation built on Nov. 2, 2019, 1:47 p.m.