stringSim {MKomics}

Function to compute similarity scores between strings

Description

The function can be used to compute similarity scores between strings.

Usage

stringSim(x, y, global = TRUE, match = 1, mismatch = -1, gap = -1, minSim = 0)

Arguments

x

character vector, first string

y

character vector, second string

global

logical; global or local alignment

match

numeric, score for a match between symbols

mismatch

numeric, score for a mismatch between symbols

gap

numeric, penalty for inserting a gap

minSim

numeric, used as required minimum score in case of local alignments

Details

The function computes optimal alignment scores for global (Needleman-Wunsch) and local (Smith-Waterman) alignments with constant gap penalties.

Scoring and trace-back matrix are computed and saved in form of attributes "ScoringMatrix" and "TraceBackMatrix". The characters in the trace-back matrix reflect insertion of a gap in string y (d: deletion), match (m), mismatch (mm), and insertion of a gap in string x (i). In addition stop indicates that the minimum similarity score has been reached.

Value

stringSim returns an object of S3 class "stringSim" inherited from class "dist"; cf. dist.

Note

The function is mainly for teaching purposes.

For distances between strings and string alignments see also Bioconductor package Biostrings.

Author(s)

Matthias Kohl [e-mail]

References

R. Merkl and S. Waack (2009). Bioinformatik Interaktiv. Wiley.

See Also

dist, stringDist

Examples

x <- "GACGGATTATG"
y <- "GATCGGAATAG"

## optimal global alignment score
d <- stringSim(x, y)
d
attr(d, "ScoringMatrix")
attr(d, "TraceBackMatrix")

## optimal local alignment score
d <- stringSim(x, y, global = FALSE)
d
attr(d, "ScoringMatrix")
attr(d, "TraceBackMatrix")