DCJ-indel and DCJ-substitution distances with distinct operation costs

Poly H da Silva; Raphael Machado; Simone Dantas; Marília DV Braga

doi:10.1186/1748-7188-8-21

Algorithms for Molecular Biology

Table 4 All recombination groups that determine the deductions for computing the DCJ-substitution distance

From: DCJ-indel and DCJ-substitution distances with distinct operation costs

	Sources	Resultants	DCJ seq.	Δ _{D C J-σ}	skip if
$U$	$A A A B A B + B B A B A B$	2 ∙	o _-2	−2w
$V$	$2 A A A B A B + B B A + B B B$	4 ∙	2o_-1≺n_-2	1−4w	$w ≥ 12$
	$2 B B A B A B + A A A + A A B$	4 ∙		1−4w
$W$	$A A A B A B + B B A + A B A B A B$	3 ∙	o_-1≺n_-2	1−3w	$w ≥ 12$
	$A A A B A B + B B B + A B B A B A$	3 ∙		1−3w
	$B B A B A B + A A A + A B B A B A$	3 ∙		1−3w
	$B B A B A B + A A B + A B A B A B$	3 ∙		1−3w
	$2 A A A B A B + B B A$	$2 ∙ + A A B A B$		1−3w
	$2 A A A B A B + B B B$ >	$2 ∙ + A A A B A$		1−3w
	$2 B B A B A B + A A A$	$2 ∙ + B B B A B$		1−3w
	$2 B B A B A B + A A B$	$2 ∙ + B B A B A$		1−3w
$X 1$	$A A A + B B A B A B$	$∙ + A B A B A B$	o _-1	−w
	$A A B + B B A B A B$	$∙ + A B B A B A$		−w
	$A A A B A B + B B A$	$∙ + A B B A B A$		−w
	$A A A B A B + B B B$	$∙ + A B A B A B$		−w
	$A A A B + B B A B A B$	∙+∙		−w
	$A A A B A B + B B A B$	∙+∙		−w
	$A A A B + B B A B$	∙+∙		−w
	$A A A B A + B B A B A B$	∙+∙		−w
	$A A B A B + B B A B A B$	∙+∙		−w
	$A A A B A B + B B A B A$	∙+∙		−w
	$A A A B A B + B B B A B$	∙+∙		−w
	$A A A + B B A$	∙+∙		−w
	$A A B + B B B$	∙+∙		−w
	$A A A + B B A B$	∙+∙		−w
	$A A B + B B A B$	∙+∙		−w
	$A A A B + B B A$	∙+∙		−w
	$A A A B + B B B$	∙+∙		−w
	$A A A + B B A B A$	∙+∙		−w
	$A A B + B B B A B$	∙+∙		−w
	$A A A B A + B B A$	∙+∙		−w
	$A A B A B + B B B$	∙+∙		−w
$X 2$	$A A A B A B + A A A B A B$	$A A A B A + A A B A B$	n _-2	1−2w	$w ≥ 12$
	$B B A B A B + B B A B A B$	$B B A B A + B B B A B$		1−2w
	$A A A B A B + A B A B A B$	$∙ + A A A B A$		1−2w
	$A A A B A B + A B B A B A$	$∙ + A A B A B$		1−2w
	$B B A B A B + A B A B A B$	$∙ + B B B A B$		1−2w
	$B B A B A B + A B B A B A$	$∙ + B B A B A$		1−2w
	$A B A B A B + A B B A B A$	∙+∙		1−2w
$Y$	$2 A B A B A B + A A B + B B A$	4 ∙	2n_-1≺o_-2	2−4w	$w ≥ 12$
	$2 A B B A B A + A A A + B B B$	4 ∙		2−4w
$Z 1$	$A B A B A B + A A A B + B B A B A$	3 ∙	n_-1≺o_-1	1−2w	$w ≥ 12$
	$A B B A B A + A A A B + B B B A B$	3 ∙		1−2w
	$A B B A B A + A A A B A + B B A B$	3 ∙		1−2w
	$A B A B A B + A A B A B + B B A B$	3 ∙		1−2w
	$A B A B A B + A A B + B B A B A$	3 ∙		1−2w
	$A B A B A B + A A B A B + B B A$	3 ∙		1−2w
	$A B B A B A + A A A + B B B A B$	3 ∙		1−2w
	$A B B A B A + A A A B A + B B B$	3 ∙		1−2w
	$A B A B A B + A A B + B B A$	$2 ∙ + A B B A B A$		1−2w
	$A B B A B A + A A A + B B B$	$2 ∙ + A B A B A B$		1−2w
$Z 2$	$2 A B A B A B + A A B$	$2 ∙ + A A A B A$	n_-1≺n_-2	2−3w	$w ≥ 23$
	$2 A B A B A B + B B A$	$2 ∙ + B B B A B$		2−3w
	$2 A B B A B A + A A A$	$2 ∙ + A A B A B$		2−3w
	$2 A B B A B A + B B B$	$2 ∙ + B B A B A$		2−3w

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ISSN: 1748-7188

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