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.

Examples

data(blosum50)
needwunsQS( "PAWHEAE", "HEAGAWGHEE", blosum50 )

[Package Biostrings version 2.0.3 Index]