Description Usage Arguments Details Value Note Author(s) References See Also Examples
Function computes an optimal global or local alignment based on a trace back
matrix as provided by function stringDist
or stringSim
.
1 |
D |
object of class |
global |
logical, global or local alignment |
Computes one possible optimal global or local alignment based on the trace back
matrix saved in an object of class "stringDist"
or "stringSim"
.
matrix: pairwise global/local alignment
The function is mainly for teaching purposes.
For distances between strings and string alignments see Bioconductor package Biostrings.
Matthias Kohl Matthias.Kohl@stamats.de
R. Merkl and S. Waack (2009). Bioinformatik Interaktiv. Wiley.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 | x <- "GACGGATTATG"
y <- "GATCGGAATAG"
## Levenshtein distance
d <- stringDist(x, y)
## optimal global alignment
traceBack(d)
## Optimal global alignment score
d <- stringSim(x, y)
## optimal global alignment
traceBack(d)
## Optimal local alignment score
d <- stringSim(x, y, global = FALSE)
## optimal local alignment
traceBack(d, global = FALSE)
|
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