Restricted DCJ-Indel Model Revisited

@inproceedings{Braga2013RestrictedDM,
  title={Restricted DCJ-Indel Model Revisited},
  author={Mar{\'i}lia Dias Vieira Braga and Jens Stoye},
  booktitle={BSB},
  year={2013}
}
The Double Cut and Join (DCJ) is a generic operation representing many rearrangements that can change the organization of a genome, but not its content. For comparing two genomes with unequal contents, in addition to DCJ operations, we have to allow insertions and deletions of DNA segments. The distance in the so-called general DCJ-indel model can be exactly computed, but allows circular chromosomes to be created at intermediate steps, even if the compared genomes are linear. In this case it is… 

Sorting Linear Genomes with Rearrangements and Indels

  • M. D. BragaJ. Stoye
  • Biology
    IEEE/ACM Transactions on Computational Biology and Bioinformatics
  • 2015
TLDR
A very simple proof is presented showing that the distance, which can be computed in linear time, is the same for both the unrestricted and the restricted DCJ-indel models.

Rearrangement Problems with Duplicated Genomic Markers

TLDR
This work aims at designing means to evaluate relative evolutionary distances between species, or to infer common ancestor genomes to a group of species, in the particular case where genomes present multiple occurrencies of genes, which makes things more complex.

On Distance and Sorting of the Double Cut-and-Join and the Inversion-*indel* Model

In der vergleichenden Genomik werden zwei oder mehrere Genome hinsichtlich ihres Verwandtschaftsgrades verglichen. Das Ziel dieser Arbeit ist die Erforschung von mathematischen Modellen, die zum

References

SHOWING 1-10 OF 27 REFERENCES

Restricted DCJ-indel model: sorting linear genomes with DCJ and indels

TLDR
A sorting algorithm is developed and a tight upper bound is given for the restricted DCJ-indel distance, which is needed for sorting linear genomes with unequal contents.

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

TLDR
The DCJ-indel and theDCJ-substitution models are extended, considering that the content-modifying cost is distinct from and upper bounded by the DCJ cost, and it is shown that the distance in both models can still be computed in linear time.

On the inversion-indel distance

TLDR
The inversion distance can be computed in a simpler way with the help of the DCJ operation and a lower and an upper bound for the inversion-indel distance in the presence of bad components are given.

DCJ Path Formulation for Genome Transformations which Include Insertions, Deletions, and Duplications

TLDR
"ghost adjacencies" are introduced to supply the missing gene ends in the genome not containing them to close paths that were due to incomplete matching, just as null points enable us to close even paths terminating in telomeres.

Genome dedoubling by DCJ and reversal

TLDR
The Genome Dedoubling Problem is presented, and two algorithms solving the problem are described in the Double-Cut-and-Join and the reversal rearrangement models, and the usefulness of the problems and the methods are showed through an application to real Drosophila data.

On the weight of indels in genomic distances

TLDR
This study discusses the disruption of the triangular inequality in some of the available methods and gives a framework to establish an efficient correction for two models recently proposed, one that includes insertions, deletions and double cut and join (DCJ) operations, and one that including substitutions and DCJ operations.

Double Cut and Join with Insertions and Deletions

TLDR
This work gives the first linear time algorithm to compute the distance between two multichromosomal genomes with unequal content, but without duplicated markers, considering insertions, deletions and double cut and join (DCJ) operations.

Genomic distance under gene substitutions

TLDR
A linear time algorithm is given to compute the genomic distance considering substitutions and double-cut-and-join (DCJ) operations to handle genomes free of duplicated markers, providing a parsimonious genomic distance that is in practice a lower bound to the real genomic distances.

Efficient sorting of genomic permutations by translocation, inversion and block interchange

TLDR
A universal double-cut-and-join operation that accounts for inversions, translocations, fissions and fusions, but also produces circular intermediates which can be reabsorbed, which converts one multi-linear chromosome genome to another in the minimum distance.

Multichromosomal median and halving problems under different genomic distances

TLDR
This theoretical study clears up a wide swathe of the algorithmical study of genome rearrangements with multiple multichromosomal genomes by settling the complexity of several genome median and halving problems, including a surprising polynomial result for the breakpoint median and guided halvingblems in genomes with circular and linear chromosomes.