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On the family-free DCJ distance and similarity

Fábio V Martinez, Pedro Feijão, Marília DV Braga, Jens Stoye
2015 Algorithms for Molecular Biology  
We also study a family-free DCJ similarity and prove that its computation is NP-hard.  ...  We prove that this new family-free DCJ distance problem is APX-hard and provide an integer linear program to its solution.  ...  Acknowledgements We would like to thank Tomáš Vinař who suggested that the NP-hardness of FFDCJ-DISTANCE could be proven via a reduction from the exemplar distance problem. FVM  ... 
doi:10.1186/s13015-015-0041-9 pmid:25859276 pmcid:PMC4391664 fatcat:lzb5wzjafbgunnu6vyrfklsb2e

Natural family-free genomic distance

Diego P. Rubert, Fábio V. Martinez, Marília D. V. Braga
2021 Algorithms for Molecular Biology  
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  ...  and join (DCJ) operation, and content-modifying insertions and deletions of DNA segments.  ...  Acknowledgements We thank the anonymous reviewers for their valuable comments. We also thank L. Bohnenkämper for sharing with us the gene families used in the analysis of Drosophila genomes with Ding.  ... 
doi:10.1186/s13015-021-00183-8 pmid:33971908 fatcat:7iv3fchvubcela7icmkwzc5fr4

Natural family-free genomic distance [article]

Diego P. Rubert and Fábio V. Martinez and Marília D. V. Braga
2020 arXiv   pre-print
On the one hand the computation of genomic distances in the family-free setting helps to match occurrences of duplicated genes and find homologies, but on the other hand this computation is NP-hard.  ...  general family-free genomic distance, providing an efficient ILP formulation to solve it.  ...  computing the unweighted family-free DCJ distance dcj (A Mn , B Mn ) ≤ d id dcj (A Mn−1 , B Mn−1 ).  ... 
arXiv:2007.03556v2 fatcat:mrcljh5hzba6niyktquxtusicm

Natural Family-Free Genomic Distance

Diego P. Rubert, Fábio V. Martinez, Marília D. V. Braga, Nadia Pisanti, Carl Kingsford
2020 Workshop on Algorithms in Bioinformatics  
This model represents structural rearrangements by the generic double cut and join (DCJ) operation and is then called family-free DCJ distance.  ...  It computes the DCJ distance between the two genomes by searching for a matching of their genes based on the given pairwise similarities, therefore helping to find gene homologies.  ...  By letting structural rearrangements be represented by the generic double cut and join (DCJ) operation [24] , a first family-free genomic distance, called family-free DCJ distance, was already proposed  ... 
doi:10.4230/lipics.wabi.2020.3 dblp:conf/wabi/RubertMB20 fatcat:sgfrs3yqonfkppwa2ulqyka2mm

Computing the family-free DCJ similarity

Diego P. Rubert, Edna A. Hoshino, Marília D. V. Braga, Jens Stoye, Fábio V. Martinez
2018 BMC Bioinformatics  
This provides a basis for further studies on the applicability and model refinement of family-free whole genome similarity measures.  ...  This problem is called family-free DCJ similarity.  ...  Acknowledgements We would like to thank Pedro Feijão and Daniel Doerr for helping us with hints on how to get simulated and real data for our experiments.  ... 
doi:10.1186/s12859-018-2130-5 pmid:29745861 pmcid:PMC5998916 fatcat:xlaehuerbzaknnqn5y43tk7qam

Small Parsimony for Natural Genomes in the DCJ-Indel Model [article]

Daniel Doerr, Cedric Chauve
2021 arXiv   pre-print
The evolutionary model that we consider is the DCJ-indel model that includes the Double-Cut and Join rearrangement operation and the insertion and deletion of genome segments.  ...  The problem aims at finding the gene orders at internal nodes of a given phylogenetic tree such that the overall genome rearrangement distance along the tree branches is minimized.  ...  Problem 1 (DCJ indel distance [10] ). Given two genomes A, B and an {A, B}resolved family assignment f , calculate the DCJ indel distance d DCJ−ID (A, B).  ... 
arXiv:2108.04297v1 fatcat:qxsghaisabgkdirsqloyijoy4i

AliquotG: An Improved Heuristic Algorithm for Genome Aliquoting

Zelin Chen, Shengfeng Huang, Yuxin Li, Anlong Xu, Marc Robinson-Rechavi
2013 PLoS ONE  
We used the new algorithm to calculate the DCJ distance between three modern vertebrate genomes and their 2R-WGD ancestor and found that the rearrangement rate might have slowed down significantly since  ...  Though several heuristic algorithms have been published, here, we sought improved algorithms for the problem with respect to the double cut and join (DCJ) distance.  ...  Acknowledgments We thank Robert Warren and David Sankoff for supplying their program. Author Contributions Conceived and designed the experiments: ZL SH AX. Analyzed the data: ZC SH.  ... 
doi:10.1371/journal.pone.0064279 pmid:23691189 pmcid:PMC3653901 fatcat:bymxrgzicbeurmsrxofm6x4g3a

The Potential of Family-Free Genome Comparison [chapter]

Marília D. V. Braga, Cedric Chauve, Daniel Doerr, Katharina Jahn, Jens Stoye, Annelyse Thévenin, Roland Wittler
2013 Models and Algorithms for Genome Evolution  
We study the potential of several family-free approaches in detecting conserved structures, genome rearrangements and in reconstructing ancestral gene orders.  ...  While the biological concept of gene families is well established, their computational prediction remains unreliable.  ...  AT is a research fellow of the Alexander von Humboldt Foundation.  ... 
doi:10.1007/978-1-4471-5298-9_13 fatcat:2rl74rvbpbgmbheisbixgrqbby

Approximating the DCJ distance of balanced genomes in linear time

Diego P. Rubert, Pedro Feijão, Marília Dias Vieira Braga, Jens Stoye, Fábio Henrique Viduani Martinez
2017 Algorithms for Molecular Biology  
to the DCJ distance problem.  ...  number of DCJ operations that transform one genome into the other.  ...  Availability of data and materials Source code of the implementation of our algorithm is available from https://  ... 
doi:10.1186/s13015-017-0095-y pmid:28293275 pmcid:PMC5345319 fatcat:zhbdnvrqpbcmtij255tmf4kowq

Constraints on genes shape long-term conservation of macro-synteny in metazoan genomes

Jie Lv, Paul Havlak, Nicholas H Putnam
2011 BMC Bioinformatics  
Results: We examine a family of simple (one-parameter) extensions of DCJ to identify models and choices of parameters consistent with the levels of macro-and micro-synteny conservation observed among animal  ...  Our software implements a flexible strategy for incorporating genomic context into the DCJ model to incorporate various types of genomic context ("DCJ-[C]"), and is available as open source software from  ...  Acknowledgements Authors' contributions NHP, PH and JL conceived the research. NHP, JL and PH wrote the software. JL carried out the simulations and genome comparisons. NHP, PH and JL wrote the paper.  ... 
doi:10.1186/1471-2105-12-s9-s11 pmid:22151646 pmcid:PMC3283319 fatcat:o2sza3vusvbknnr3cr4arkbvda

Tractability results for the Double-Cut-and-Join circular median problem [article]

Ahmad Mahmoody-Ghaidary and Cedric Chauve and Ladislav Stacho
2011 arXiv   pre-print
The circular median problem in the Double-Cut-and-Join (DCJ) distance asks to find, for three given genomes, a fourth circular genome that minimizes the sum of the mutual distances with the three other  ...  ones.  ...  C.C. and L.S. are supported by NSERC Discovery Grants. References  ... 
arXiv:1111.5872v1 fatcat:u5uzcs4rtncq5nzblsla5khmfe

Rearrangement Problems with Duplicated Genomic Markers [article]

Antoine Thomas
2014 arXiv   pre-print
A major goal of the field is to establish evolutionary relationships within groups of species, in order to infer the topology of an evolutionary tree formed by this group and common ancestors to some of  ...  Several hypotheses accounting for the presence of duplications were considered. Distances formulae as well as scenario computing algorithms were established, along with their complexity proofs.  ...  We begin by recalling some useful definitions and properties of the DCJ operations that allow one to decrease the DCJ halving distance by 1 in the resulting genome.  ... 
arXiv:1410.5415v1 fatcat:t3slxmig65a6rihwxgvp66xqlu

Analysis of Gene Order Evolution Beyond Single-Copy Genes [chapter]

Nadia El-Mabrouk, David Sankoff
2012 Msphere  
We then consider three levels of gene organization: the gene family level (evolution by duplication, loss and speciation), the cluster level (evolution by tandem duplications) and the genome level (all  ...  the problems of orthology, paralogy and synteny block identification.  ...  See Figure 1 (right) for an example of the DCJ distance.  ... 
doi:10.1007/978-1-61779-582-4_15 pmid:22407718 fatcat:kerbedfsgrgi5npicdlbd6u4aa

Gene family assignment-free comparative genomics

Daniel Doerr, Annelyse Thévenin, Jens Stoye
2012 BMC Bioinformatics  
As a case study, we present a new similarity measure between pairs of genomes that is related to the breakpoint distance. We propose an exact and a heuristic algorithm for its computation.  ...  Since such information is hard to obtain, it is common to predict homologous groups based on sequence similarity. These hypothetical groups of homologous genes are called gene families.  ...  Problem 1 (Family-free(FF)-Adjacencies) Given two genomes G 1 and G 2 , a normalized similarity measure s, and some a Î ]0, 1], find a matching Min B = (G 1 , G 2 ,E) such that at least one edge per connected  ... 
doi:10.1186/1471-2105-13-s19-s3 pmid:23281826 pmcid:PMC3526435 fatcat:ydnaay67w5bc7geypzikzhfbv4

A Tractable Variant of the Single Cut or Join Distance with Duplicated Genes [chapter]

Pedro Feijão, Aniket Mane, Cedric Chauve
2017 Lecture Notes in Computer Science  
We prove that in this model, computing the distance and a parsimonious evolutionary scenario in terms of SCJ and single-gene duplication events can be done in linear time.  ...  We also show that the median problem is tractable for this distance.  ...  CC is supported by a Discovery Grant from the Natural Sciences and Engineering Research Council of Canada. PF is supported by the Genome Canada grant PathoGiST.  ... 
doi:10.1007/978-3-319-67979-2_2 fatcat:h5fgl3ojsneftmj3fheiml5jsm
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