Calculate pairwise percent identity between two sequences
Usage
calculate_pid(
seq1,
seq2,
substitutionMatrix = "BLOSUM62",
gapOpening = 10,
gapExtension = 0.5,
type = "global",
...
)
Arguments
- seq1
First sequence
- seq2
Second sequence
- substitutionMatrix
Substitution matrix to use for alignment
- gapOpening
Gap opening penalty
- gapExtension
Gap extension penalty
- type
Type of alignment. One of "global", "local", "overlap"
- ...
Additional arguments passed to pwalign::pairwiseAlignment
Value
Pairwise percent identity