align_multi: Align multiple sequences to reference

In t-arae/bstringr: A package to use a character vector as a biological strings

Description

Align multiple sequences to reference

Usage

bstr_align_multi(sub, pat, type = "global", gapO = 10, gapE = 4)

dstr_align_multi(sub, pat, rc, type = "global", gapO = 10, gapE = 4)

Arguments

sub	a subject sequence
pat	pattern sequence
type	type of alignment. One of "global", "local", "overlap", "global-local", and "local-global".
gapO	gap opening penalty
gapE	gap extension penalty
rc	logical value. if TRUE, the seq2 is aligned after reverse complemented. default is FALSE.

Examples

ref <- c(reference = "abcdefghijk")
patterns <- c(one = "abc", two = "d", three = "efgjk")
bstr_align_multi(ref, patterns)

ref <- c(ref = "AAACCCTTTGGG")
patterns <- c(A = "AAA", C = "CCC", T = "TTT", G = "GGG")
dstr_align_multi(ref, patterns)
dstr_align_multi(ref, patterns, 1:2)
dstr_align_multi(ref, patterns, c("T", "G"))

t-arae/bstringr documentation built on March 18, 2021, 3:08 a.m.