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

@article{Yancopoulos2005EfficientSO, title={Efficient sorting of genomic permutations by translocation, inversion and block interchange}, author={Sophia Yancopoulos and Oliver Attie and Richard Friedberg}, journal={Bioinformatics}, year={2005}, volume={21 16}, pages={ 3340-6 } }

MOTIVATION
Finding genomic distance based on gene order is a classic problem in genome rearrangements. Efficient exact algorithms for genomic distances based on inversions and/or translocations have been found but are complicated by special cases, rare in simulations and empirical data. We seek a universal operation underlying a more inclusive set of evolutionary operations and yielding a tractable genomic distance with simple mathematical form.
RESULTS
We study a universal double-cut-and…

## 462 Citations

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The algorithmic study of this new model of genome rearrangement, namely the inverse tandem duplication random loss (iTDRL) model, is initiated by proving that a shortest rearrangements scenario that transforms one given gene order into another given gene orders can be obtained in quasilinear time.

### Sorting by Weighted Reversals, Transpositions, and Inverted Transpositions

- BiologyRECOMB
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This paper provides a 1.5-approximation algorithm for sorting by weighted reversals, transpositions and inverted transposition for biologically realistic weights in order to reconstruct ancient events in the evolutionary history of organisms.

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The signed reversal and transposition distance between two genomes considering their intergenic regions is investigated and two approximation algorithms are developed, which check how these algorithms behave when assigning weights for genome rearrangements.

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- BiologyBMC Bioinformatics
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This paper presents a heuristic algorithm to sort an ancestral genome into a genome of a descendant (with arbitrary gene content) by reversals, block interchanges, tandem duplications, and deletions, where tandem duplication and deletion are of arbitrary size.

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### Sorting by Weighted Reversals and Transpositions

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This study studies the Sorting by Weighted Reversals and Transpositions problem on signed permutations and develops a generic approximation algorithm to deal with different weights for reversals and transpositions.

### An Experimental Evaluation of Inversion-and Transposition-Based Genomic Distances through Simulations

- Biology2007 IEEE Symposium on Computational Intelligence and Bioinformatics and Computational Biology
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The main finding is that inversion and DCJ measures return very similar results even on data generated using only transpositions, while the measure based on Hartman's bound is often too loose to provide comparable accuracy in genomic comparisons or phylogenetic reconstruction.

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An easy-to-compute formula is given that corresponds to the exact number of optimal DCJ sorting sequences for a particular subset of instances of the problem and the demonstration of the possibility of obtaining one optimal sorting sequence by properly replacing any pair of consecutive operations in another optimal sequence.

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