Yancopoulos2008

CREATED: 200810200701 Title: Sorting Genomes with Insertions, Deletions and Duplications by DCJ ** Adjacency graph <-dual-> Breakpoint graph

• see Bergeron et al. 2006, unifying view of genome rearrangements
• symmetric and combines both forward and backward breakpoint graph
• handles circular genomes, D = N - C
• extensions: closing paths to from cycles ** Dealing with linear genomes
• caps, fictional elements?
• null chromosomes, only two caps
• D = N - C ** Insertions and deletions
• ghost vertex -> affects triangle inequality
• D = N - C? Doesn’t work with ghosts -> allows free lunch
• fix is to charge for ghosts (surcharge rule), need to pay for ghosts (ghostly 1 cycle)
• nughs: half null, half ghost, causes more problems, can reduce dist ** Dealing with multiple copies
• multiple choice adjacency graph