Models and Algorithms for Genome Evolution by Cedric Chauve Nadia El-Mabrouk & Eric Tannier

Author:Cedric Chauve, Nadia El-Mabrouk & Eric Tannier
Language: eng
Format: epub
Publisher: Springer London, London

D. Bader, M. Yan, and B. Moret [2] later showed that this edit distance can be computed in linear time. Extending this distance to multichromosomal genomes can be done through a reduction to the unichromosomal case using “capping,” a subtle process that required several iterations before it was done right [3, 33, 38, 93]. The various operations supported under this multichromosomal model (for which see the next section), all of which keep the gene content intact, give rise to what we shall call the HP-distance. The transposition distance is known to be NP-hard to compute [8]; attempts at defining distances combining transpositions and inversions have so far proved unsuccessful.

Moving to distances between genomes of unequal gene content has proved very challenging. N. El-Mabrouk [25] first extended the results of S. Hannenhalli and P. Pevzner to the computation of edit distances for inversions and deletions and gave a heuristic for inversions, deletions, and non-duplicating insertions. The distance computation is NP-hard when duplications and inversions are present [12]. M. Marron et al. [48] gave a guaranteed approximation for edit distances under arbitrary operations (including duplications and deletions).

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