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The Breakpoint Graph. 1 5- 2- 4 3 . The Breakpoint Graph. 6 1 5- 2- 4 3 0. Augment with 0 = n+1. The Breakpoint Graph.

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the breakpoint graph1
The Breakpoint Graph

6 1 5- 2- 4 3 0

  • Augment with 0 = n+1
the breakpoint graph2
The Breakpoint Graph

11 2 1 9 10 3 4 8 7 6 5 0

6 1 5- 2- 4 3 0

  • Augment with 0 = n+1
  • Vertices 2i, 2i-1 for each i
the breakpoint graph3
The Breakpoint Graph

11 2 1 9 10 3 4 8 7 6 5 0

6 1 5- 2- 4 3 0

  • Augment with 0 = n+1
  • Vertices 2i, 2i-1 for each i
  • Blue edges between adjacent vertices
the breakpoint graph4
The Breakpoint Graph

11 2 1 9 10 3 4 8 7 6 5 0

6 1 5- 2- 4 3 0

  • Augment with 0 = n+1
  • Vertices 2i, 2i-1 for each i
  • Blue edges between adjacent vertices
  • Red edges between consecutive labels 2i,2i+1
slide6

Sort a given breakpoint graph

11 2 1 9 10 3 4 8 7 6 5 0

into n+1 trivial cycles

11 10 9 8 7 6 5 4 3 2 1 0

slide7

Sort a given breakpoint graph

11 2 1 9 10 3 4 8 7 6 5 0

into n+1 trivial cycles

11 10 9 8 7 6 5 4 3 2 1 0

Conclusion:We want to increase number of cycles

slide8

Def:A reversal acts on two blue edges

11 2 1 9 10 3 4 8 7 6 5 0

cutting them and re-connecting them

11 2 1 9 10 3 4 7 8 6 5 0

slide9

A reversal can either

11 2 1 9 10 3 4 8 7 6 5 0

Act on two cycles, joining them (bad!!)

11 2 1 9 10 3 4 7 8 6 5 0

slide10

A reversal can either

11 2 1 9 10 3 4 8 7 6 5 0

Act on one cycle, changing it (profitless)

11 2 1 5 6 7 8 4 3 10 9 0

slide11

A reversal can either

11 2 1 9 10 3 4 8 7 6 5 0

Act on one cycle, splitting it (good move)

11 10 9 1 2 3 4 8 7 6 5 0

basic theorem
Basic Theorem

(Bafna, Pevzner 93)

Where d=#reversals needed (reversal distance),

and c=#cycles.

Proof: Every reversal changes c by at most 1.

basic theorem1
Basic Theorem

(Bafna, Pevzner 93)

Where d=#reversals needed (reversal distance),

and c=#cycles.

Proof: Every reversal changes c by at most 1.

Alternative formulation:

where b=#breakpoints, and c ignores short cycles

oriented edges
Oriented Edges

Red edges can be :

Oriented{

Right-to-Right

Left-to-Left

Unoriented{

Left-to-Right

Right-to-Left

oriented edges1
Oriented Edges

Red edges can be :

Oriented{

Right-to-Right

Left-to-Left

Unoriented{

Left-to-Right

Right-to-Left

Def:This reversal acts on the red edge

oriented edges2
Oriented Edges

Red edges can be :

Oriented{

Right-to-Right

Left-to-Left

Unoriented{

Left-to-Right

Right-to-Left

Def:This reversal acts on the red edge

Thm: A reversal acting on a red edge is good

the edge is oriented

overlapping edges
Overlapping Edges

Def: Two red edges are said to be overlapping if they span intersecting intervals which do not contain one another.

overlapping edges1
Overlapping Edges

Def: Two red edges are said to be overlapping if they span intersecting intervals which do not contain one another The lines intersect

overlapping edges2
Overlapping Edges

Def: Two red edges are said to be overlapping if they span intersecting intervals which do not contain one another The lines intersect

Thm: A reversal acting on a red edge flips the orientation of all edges overlapping it, leaving other orientations unchanged

overlapping edges3
Overlapping Edges

Def: Two red edges are said to be overlapping if they span intersecting intervals which do not contain one another The lines intersect

Thm: if e,f,g overlap each other, then after applying a reversal that acts on e,f and g do not overlap

overlap graph
Overlap Graph

Nodes correspond to red edges.

Two nodes are connected by an arc if they overlap

overlap graph1
Overlap Graph

Nodes correspond to red edges.

Two nodes are connected by an arc if they overlap

Def:Unoriented connected components in the overlap graph - all nodes correspond to oriented edges.

overlap graph2
Overlap Graph

Nodes correspond to red edges.

Two nodes are connected by an arc if they overlap

Def:Unoriented connected components in the overlap graph - all nodes correspond to oriented edges.

Cannot be solved in only good moves

dealing with unoriented components
Dealing with Unoriented Components
  • A profitless move on an oriented edge, making its component to oriented
dealing with unoriented components1
Dealing with Unoriented Components
  • A profitless move on an oriented edge, making its component to oriented

or:

  • A bad move (reversal) joining cycles from different unoriented components, thus merging them flipping the orientation of many components on the way
hurdles
Hurdles
  • Def:Hurdle - an unoriented connected component which is consecutive along the cycle
hurdles1
Hurdles
  • Def:Hurdle - an unoriented connected component which is consecutive along the cycle
  • Thm: (Hannenhalli, Pevzner 95)

Proof: A hurdle is destroyed by a profitless move, or

at most two are destroyed (merged) by a bad move.

hurdles2
Hurdles
  • Def:Hurdle - an unoriented connected component which is consecutive along the cycle
  • Thm: (Hannenhalli, Pevzner 95)

Proof: A hurdle is destroyed by a profitless move, or

at most two are destroyed (merged) by a bad move.

  • Thm:
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