dada2: nwhamming – R documentation

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nwhamming

Hamming distance after Needlman-Wunsch alignment.

Description

This function performs a Needleman-Wunsch alignment between two sequences, and then counts the number of mismatches and indels in that alignment. End gaps are not included in this count.

Usage

nwhamming(s1, s2, ...)

Arguments

`s1`	(Required). `character(1)`. The first sequence to align. A/C/G/T only.
`s2`	(Required). `character(1)`. The second sequence to align. A/C/G/T only.
`...`	(Optional). Further arguments to pass on to `nwalign`.

Value

integer(1). The total number of mismatches and gaps, excluding gaps at the beginning and end of the alignment.

Examples

sq1 <- "CTAATACATGCAAGTCGAGCGAGTCTGCCTTGAAGATCGGAGTGCTTGCACTCTGTGAAACAAGATA"
 sq2 <- "TTAACACATGCAAGTCGAACGGAAAGGCCAGTGCTTGCACTGGTACTCGAGTGGCGAACGGGTGAGT"
nwhamming(sq1, sq2)
nwhamming(sq1, sq2, band=16)

dada2

Accurate, high-resolution sample inference from amplicon sequencing data

v1.18.0

LGPL-3

Authors

Benjamin Callahan <benjamin.j.callahan@gmail.com>, Paul McMurdie, Susan Holmes

Initial release

2020-08-07