Approximating the DCJ distance of balanced genomes in linear time

Rubert, Diego P.; Feijão, Pedro; Braga, Marília D. V.; Stoye, Jens; Martinez, Fábio Henrique Viduani

doi:10.1186/s13015-017-0095-y

Cited by 13 publications

(9 citation statements)

References 16 publications

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“…Moreover, one can directly correlate the problem to the adjacency similarity problem, where the goal is to maximize the number of preserved adjacencies between two given genomes [ 11 , 19 ]. However, since there the objective is to maximize the number of cycles of length 2, even an approximation for the adjacency similarity problem is not a good algorithm for the FFDCJ-SIMILARITY problem, where cycles of higher lengths are possible in the solution [ 20 ].…”

Section: Methodsmentioning

confidence: 99%

Computing the family-free DCJ similarity

et al. 2018

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BackgroundThe genomic similarity is a large-scale measure for comparing two given genomes. In this work we study the (NP-hard) problem of computing the genomic similarity under the DCJ model in a setting that does not assume that the genes of the compared genomes are grouped into gene families. This problem is called family-free DCJ similarity.ResultsWe propose an exact ILP algorithm to solve the family-free DCJ similarity problem, then we show its APX-hardness and present four combinatorial heuristics with computational experiments comparing their results to the ILP.ConclusionsWe show that the family-free DCJ similarity can be computed in reasonable time, although for larger genomes it is necessary to resort to heuristics. This provides a basis for further studies on the applicability and model refinement of family-free whole genome similarity measures.Electronic supplementary materialThe online version of this article (10.1186/s12859-018-2130-5) contains supplementary material, which is available to authorized users.

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Section: Methodsmentioning

confidence: 99%

Computing the family-free DCJ similarity

et al. 2018

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“…We have presented an approximation algorithm for computing the family-based DCJ distance between two balanced 1 unichromosomal genomes with at most k copies of each gene [Rubert et al 2016, Rubert et al 2017a, an NP-hard problem [Shao et al 2015]. The main step of the approximation algorithm relies on an approximation for an related problem, the Breakpoint Distance (BD), and on decomposing a special bipartite graph called adjacency graph (AG) into cycles.…”

Section: Family-based Dcj Distancementioning

confidence: 99%

“…Algorithms for Molecular Biology, 2017. [Rubert et al 2017a] 2. Computing the family-free DCJ similarity.…”

Section: Publications In Journalsmentioning

confidence: 99%

Distance and Similarity Measures in Comparative Genomics

Rubert¹,

Stoye²,

Martinez³

2020

Anais Do Concurso De Teses E Dissertações Da SBC (CTD-SBC 2020)

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Research in comparative genomics supports the investigation of important questions in molecular biology, genetics and biomedicine. A central question in this field is the elucidation of similarities and differences between genomes by means of different measures. This summary, submitted to CTD 2020, briefly describes the main contributions, originality and impact possibilities of the thesis entitled "Distance and Similarity Measures in Comparative Genomics", by Diego P. Rubert.

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“…Without duplications, that is, with the additional restriction that each family occurs at most once in each genome, many polynomial models have been proposed to compute the genomic distance [2][3][4][5][6]. However, when duplications are allowed the problem is more intricate and all approaches proposed so far are NP-hard, see for instance [7][8][9][10][11][12].…”

Section: Introductionmentioning

confidence: 99%

Natural Family-Free Genomic Distance

Rubert

Martinez

Braga

2021

Preprint

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Background: A classical problem in comparative genomics is to compute the rearrangement distance, that is the minimum number of large-scale rearrangements required to transform a given genome into another given genome.The traditional approaches in this area are family-based, i.e., require the classification of DNA fragments of both genomes into families. Furthermore, the most elementary family-based models, which are able to compute distances in polynomial time, restrict the families to occur at most once in each genome. In contrast, the distance computation in models that allow multifamilies (i.e., families with multiple occurrences) is NP-hard. Very recently, Bohnenkamper etal. (J. Comput. Biol., 2020) proposed an ILP formulation for computing the genomic distance of genomes with multifamilies, allowing structural rearrangements, represented by the generic double cut and join (DCJ) operation, and content-modifying insertions and deletions of DNA segments. This ILP is very efficient, but must maximize a matching of the genes in each multifamily, in order to prevent the free lunch artifact that would otherwise let empty or almostempty matchings give smaller distances. Results: In this paper, we adopt the alternative family-free setting that, instead of family classification, simply uses the pairwise similarities between DNA fragments of both genomes to compute their rearrangement distance. We adapted the ILP mentioned above and developed a model in which pairwise similarities are used to assign weights to both matched and unmatched genes, so that an optimal solution does not necessarily maximize the matching. Our modelthen results in a natural family-free genomic distance, that takes into consideration all given genes, without prior classification into families, and has a search space composed of matchings of any size. In spite of its bigger searchspace, our ILP seems to be boosted by a reduction of the number of co-optimal solutions due to the weights. Indeed, it converged faster than the original one by Bohnenkamper et al. for instances with the same number of multipleconnections. We can handle not only bacterial genomes, but also fungi and insects, or sets of chromosomes of mammals and plants. In a comparison study of six fruit fly genomes, we obtained accurate results.

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Approximating the DCJ distance of balanced genomes in linear time

Cited by 13 publications

References 16 publications

Computing the family-free DCJ similarity

Computing the family-free DCJ similarity

Distance and Similarity Measures in Comparative Genomics

Natural Family-Free Genomic Distance

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