align_pairwise: Align bstr sequence

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

Description

Align bstr sequence

Usage

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

dstr_align_pairwise(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

bstr_align_pairwise("abcdefgh", "cde")
bstr_align_pairwise("abcdefgh", "cde", type = "local")
bstr_align_pairwise("abcdefgh", c("cde", "befg"))
bstr_align_pairwise("abcdefgh", c("cde", "befg"), gapO = 0, gapE = 1)

dstr_align_pairwise("aaaccctttggg", "gggaaa")
dstr_align_pairwise("aaaccctttggg", "gggaaa", TRUE)
dstr_align_pairwise("aaaccctttggg", c("gggaaa", "cccttt"), 1)

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