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On the family-free DCJ distance and similarity
2015
Algorithms for Molecular Biology
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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
2021
Algorithms for Molecular Biology
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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]
2020
arXiv
pre-print
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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
2020
Workshop on Algorithms in Bioinformatics
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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
2018
BMC Bioinformatics
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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]
2021
arXiv
pre-print
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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
2013
PLoS ONE
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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]
2013
Models and Algorithms for Genome Evolution
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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
2017
Algorithms for Molecular Biology
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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:// git.facom.ufms.br/diego/k-dcj. ...
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
2011
BMC Bioinformatics
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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]
2011
arXiv
pre-print
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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]
2014
arXiv
pre-print
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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]
2012
Msphere
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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
2012
BMC Bioinformatics
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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]
2017
Lecture Notes in Computer Science
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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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