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 3 Path recombinations that are used to compute the DCJ-substitution distance

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

	Sources	Result.	Δσ	Δ _DCJ	Δ _DCJ-σ		Sources	Result.	Δσ	Δ _DCJ	Δ _DCJ-σ
						o _-1	$A A A + B B A B A B$	$∙ + A B A B A B$	−1	0	−w
o _-2	$A A A B A B + B B A B A B$	∙+∙	−2	0	−2w	o _-1	$A A B + B B A B A B$	$∙ + A B B A B A$	−1	0	−w
						o _-1	$A A A B A B + B B A$	$∙ + A B B A B A$	−1	0	−w
						o _-1	$A A A B A B + B B B$	$∙ + A B A B A B$	−1	0	−w
o _-1	$A A A + B B A B A$	∙+∙	−1	0	−w
o _-1	$A A B + B B B A B$	∙+∙	−1	0	−w	n _-2	$A A A B A B + A A A B A B$	$A A A B A + A A B A B$	−2	1	1−2w
o _-1	$A A A B A + B B A$	∙+∙	−1	0	−w	n _-2	$B B A B A B + B B A B A B$	$B B A B A + B B B A B$	−2	1	1−2w
o _-1	$A A B A B + B B B$	∙+∙	−1	0	−w	n _-2	$A A A B A B + A B A B A B$	$∙ + A A A B A$	−2	1	1−2w
o _-1	$A A A B + B B A B A B$	∙+∙	−1	0	−w	n _-2	$A A A B A B + A B B A B A$	$∙ + A A B A B$	−2	1	1−2w
o _-1	$A A A B A B + B B A B$	∙+∙	−1	0	−w	n _-2	$B B A B A B + A B A B A B$	$∙ + B B B A B$	−2	1	1−2w
o _-1	$A A A B + B B A B$	∙+∙	−1	0	−w	n _-2	$B B A B A B + A B B A B A$	$∙ + B B A B A$	−2	1	1−2w
o _-1	$A A A B A + B B A B A B$	∙+∙	−1	0	−w	n _-2	$A B A B A B + A B B A B A$	∙+∙	−2	1	1−2w
o _-1	$A A B A B + B B A B A B$	∙+∙	−1	0	−w
o _-1	$A A A B A B + B B A B A$	∙+∙	−1	0	−w	n _-1	$A A A + A B B A B A$	$∙ + A A A B A B$	−1	1	1−w
o _-1	$A A A B A B + B B B A B$	∙+∙	−1	0	−w	n _-1	$A A B + A B A B A B$	$∙ + A A A B A B$	−1	1	1−w
o _-1	$A A A + B B A$	∙+∙	−1	0	−w	n _-1	$B B A + A B A B A B$	$∙ + B B A B A B$	−1	1	1−w
o _-1	$A A B + B B B$	∙+∙	−1	0	−w	n _-1	$B B B + A B B A B A$	$∙ + B B A B A B$	−1	1	1−w
o _-1	$A A A + B B A B$	∙+∙	−1	0	−w	n _-1	$A A A B + A B A B A B$	$∙ + A A A$	−1	1	1−w
o _-1	$A A B + B B A B$	∙+∙	−1	0	−w	n _-1	$A A A B + A B B A B A$	$∙ + A A B$	−1	1	1−w
o _-1	$A A A B + B B A$	∙+∙	−1	0	−w	n _-1	$B B A B + A B B A B A$	$∙ + B B A$	−1	1	1−w
o _-1	$A A A B + B B B$	∙+∙	−1	0	−w	n _-1	$B B A B + A B A B A B$	$∙ + B B B$	−1	1	1−w

Recombinations of type o_{-
2}, o_{-
1} and n_{-
2} can have Δ_{DCJ
-
σ}<0. Recombinations of type n_{-
1} have Δ_{DCJ
-
σ}≥ 0, but produce an AA or a BB-path with runs $A B A B$ or $A$ or $B$ .

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ISSN: 1748-7188

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