Pairwise Sequence Alignment for Setlists

This function performs pairwise sequence alignment for setlists using dynamic programming. It calculates the optimal alignment between two sequences and returns the aligned sequences along with a similarity score.

Usage

align_pairwise_setlists(
  seq1,
  seq2,
  gap_penalty = -1,
  match_score = 2,
  mismatch_penalty = -1
)

Arguments

seq1

A character vector representing the first setlist sequence.

seq2

A character vector representing the second setlist sequence.

gap_penalty

Numeric value for the gap penalty (default: -1).

match_score

Numeric value for the match score (default: 2).

mismatch_penalty

Numeric value for the mismatch penalty (default: -1).

Value

A list containing:

seq1_aligned

The aligned sequence for seq1

seq2_aligned

The aligned sequence for seq2

similarity

A numeric value representing the similarity between the sequences

Details

Perform Pairwise Sequence Alignment for Setlists

The function uses a scoring system defined by the input parameters: - Match score (default: 2) - Mismatch penalty (default: -1) - Gap penalty (default: -1)

The alignment is performed using a dynamic programming approach with a scoring matrix and a traceback matrix to determine the optimal alignment.

Examples

seq1 <- c("A", "B", "C", "D")
seq2 <- c("A", "C", "D")
result <- align_pairwise_setlists(seq1, seq2)
print(result)
#> $seq1_aligned
#> [1] "A" "B" "C" "D"
#> 
#> $seq2_aligned
#> [1] "A" NA  "C" "D"
#> 
#> $similarity
#> [1] 0.75
#> 

# Using custom scoring parameters
result_custom <- align_pairwise_setlists(seq1, seq2, gap_penalty = -2, match_score = 3, mismatch_penalty = -2)
print(result_custom)
#> $seq1_aligned
#> [1] "A" "B" "C" "D"
#> 
#> $seq2_aligned
#> [1] "A" NA  "C" "D"
#> 
#> $similarity
#> [1] 0.75
#>