seqDist

seqDist - Calculate distance between two sequences

Description¶

seqDist calculates the distance between two DNA sequences.

seqDist(seq1, seq2, dist_mat = getDNAMatrix())

seq1: character string containing a DNA sequence.
seq2: character string containing a DNA sequence.
dist_mat: Character distance matrix. Defaults to a Hamming distance matrix returned by getDNAMatrix. If gap characters, c("-", "."), are assigned a value of -1 in dist_mat then contiguous gaps of any run length, which are not present in both sequences, will be counted as a distance of 1. Meaning, indels of any length will increase the sequence distance by 1. Gap values other than -1 will return a distance that does not consider indels as a special case.

Numerical distance between seq1 and seq2.

# Ungapped examples
seqDist("ATGGC", "ATGGG")

[1] 1

seqDist("ATGGC", "ATG??")

[1] 2


# Gaps will be treated as Ns with a gap=0 distance matrix
seqDist("ATGGC", "AT--C", dist_mat=getDNAMatrix(gap=0))

[1] 0


# Gaps will be treated as universally non-matching characters with gap=1
seqDist("ATGGC", "AT--C", dist_mat=getDNAMatrix(gap=1))

[1] 2


# Gaps of any length will be treated as single mismatches with a gap=-1 distance matrix
seqDist("ATGGC", "AT--C", dist_mat=getDNAMatrix(gap=-1))

[1] 1


# Gaps of equivalent run lengths are not counted as gaps
seqDist("ATG-C", "ATG-C", dist_mat=getDNAMatrix(gap=-1))

[1] 0


# Overlapping runs of gap characters are counted as a single gap
seqDist("ATG-C", "AT--C", dist_mat=getDNAMatrix(gap=-1))

[1] 1

seqDist("A-GGC", "AT--C", dist_mat=getDNAMatrix(gap=-1))

[1] 1

seqDist("AT--C", "AT--C", dist_mat=getDNAMatrix(gap=-1))

[1] 0


# Discontiguous runs of gap characters each count as separate gaps
seqDist("-TGGC", "AT--C", dist_mat=getDNAMatrix(gap=-1))

[1] 2