Genomic Distance with High Indel Costs

We determine complexity of computing the DCJ-indel distance, when DCJ and indel operations have distinct constant costs, by showing an exact formula that can be computed in linear time for any choice of (constant) costs for DCJ and indel operations. We additionally consider the problem of triangular inequality disruption and propose an algorithmically efficient correction on each member of the family of DCJ-indel.

[1]  Pavel A. Pevzner,et al.  Transforming cabbage into turnip: polynomial algorithm for sorting signed permutations by reversals , 1995, JACM.

[2]  Jens Stoye,et al.  Sorting Linear Genomes with Rearrangements and Indels , 2015, IEEE/ACM Transactions on Computational Biology and Bioinformatics.

[3]  David Sankoff,et al.  Edit Distance for Genome Comparison Based on Non-local Operations * 1 Role of Rearrangements in Evolution , .

[4]  Jens Stoye,et al.  The Solution Space of Sorting by DCJ , 2010, J. Comput. Biol..

[5]  Simone Dantas,et al.  DCJ-indel and DCJ-substitution distances with distinct operation costs , 2013, Algorithms for Molecular Biology.

[6]  Jens Stoye,et al.  A Unifying View of Genome Rearrangements , 2006, WABI.

[7]  Jens Stoye,et al.  On the weight of indels in genomic distances , 2011, BMC Bioinformatics.

[8]  Tao Jiang,et al.  On the complexity and approximation of syntenic distance , 1997, RECOMB '97.

[9]  Richard Friedberg,et al.  DCJ Path Formulation for Genome Transformations which Include Insertions, Deletions, and Duplications , 2009, J. Comput. Biol..

[10]  Richard Friedberg,et al.  Efficient sorting of genomic permutations by translocation, inversion and block interchange , 2005, Bioinform..

[11]  Jens Stoye,et al.  Double Cut and Join with Insertions and Deletions , 2011, J. Comput. Biol..

[12]  Pavel A. Pevzner,et al.  Transforming Cabbage into Turnip: Polynomial Algorithm for Sorting Signed Permutations by Reversals , 1999, J. ACM.