R: (Deprecated) Needleman-Wunsch Global Alignment

needwunsQS {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)

[Package Biostrings version 2.16.9 Index]