needwunsQS            package:Biostrings            R Documentation

(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.

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 '"PairwiseAlignedXStringSet"'.

Author(s):

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

References:

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

See Also:

     pairwiseAlignment, PairwiseAlignedXStringSet-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)

