Align two sequences — align • motiftools

Align two sequences using local (Smith-Waterman) or global (Needleman-Wunsch) sequence alignment.

align(
  x1,
  x2,
  score.matrix = NULL,
  gap.score = -1,
  type = "local",
  debug = FALSE
)

Arguments

x1	pattern sequence: a character vector, scalar or AAString.
x2	subject sequence: a character vector, scalar or AAString.
score.matrix	substitution matrix.
gap.score	gap score.
type	type of alignment: global or local (default: local).
debug	logical; whether to return debugging data.

Value

AlignResult object.

Examples

library(motiftools)
align("ALVDE", "AVRES", score.matrix = "BLOSUM62")
#> $alignment
#>   1   2   3   4   5  
#> x "A" "L" "V" "D" "E"
#> y "A" "-" "V" "R" "E"
#> 
#> $score
#> [1] 26
#>