needwunsQS {Biostrings}R Documentation

quadratic-space, simple gap implementation of Needleman-Wunsch global alignment algorithm

Description

quadratic-space, simple gap implementation of Needleman-Wunsch global alignment algorithm

Usage

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

Arguments

s1 s1: first string, an R character vector of length 1 or a BString instance
s2 s2: second string, same data type as s1
substmat substmat: matrix of alignment score values
gappen gappen: penalty for introducing a gap in the alignment

Details

follows specification of Durbin, Eddy, Krogh, Mitchison (1998).

Value

an instance of the S3 class ``needwunsQS'', for which there are print and alignScore methods.

Author(s)

Vince Carey <stvjc@channing.harvard.edu>

References

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

See Also

BStringAlign-class, scoring.matrices

Examples

  ## 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")

[Package Biostrings version 2.6.6 Index]