DUPCAR: Reconstructing Contiguous Ancestral Regions with Duplications

Ma, Jian; Raney, Brian J.; Suh, Bernard; Zhang, Louxin; Miller, Webb; Haussler, David

doi:10.1089/cmb.2008.0069

Cited by 54 publications

(52 citation statements)

References 33 publications

(35 reference statements)

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“…Given a set of SFs B, the SF graph is an undirected graph G = (V, E), where V = {b h , b t jb ∈ B} is the set of vertices that represents the head b h and tail b t of a SF b, and E is the set of undirected edges. The idea is analogous to the breakpoint graph that was used in genome rearrangement analysis (29,30). The edge between two SFs can be created by connecting either the head or tail vertices of each SF, which represents both the order and orientation of SFs.…”

Section: Methodsmentioning

confidence: 99%

“…The degree and cycle constraints ensure that each connected component is actually a chain of SFs (without cycle), and each SF is adjacent with only one SF. The SF ordering problem is analogous to the minimum path cover problem and it is known as NP-hard (30). Therefore, we developed a greedy algorithm as an approximate solution to solve the SF ordering problem, which constructs the chains of SFs by merging two adjacent SFs with the highest edge weight first at each step (SI Appendix).…”

Section: Methodsmentioning

confidence: 99%

See 1 more Smart Citation

Reference-assisted chromosome assembly

Kim

Larkin

Cai

et al. 2013

Proc. Natl. Acad. Sci. U.S.A.

Self Cite

117

136

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One of the most difficult problems in modern genomics is the assembly of full-length chromosomes using next generation sequencing (NGS) data. To address this problem, we developed "reference-assisted chromosome assembly" (RACA), an algorithm to reliably order and orient sequence scaffolds generated by NGS and assemblers into longer chromosomal fragments using comparative genome information and paired-end reads. Evaluation of results using simulated and real genome assemblies indicates that our approach can substantially improve genomes generated by a wide variety of de novo assemblers if a good reference assembly of a closely related species and outgroup genomes are available. We used RACA to reconstruct 60 Tibetan antelope (Pantholops hodgsonii) chromosome fragments from 1,434 SOAPdenovo sequence scaffolds, of which 16 chromosome fragments were homologous to complete cattle chromosomes. Experimental validation by PCR showed that predictions made by RACA are highly accurate. Our results indicate that RACA will significantly facilitate the study of chromosome evolution and genome rearrangements for the large number of genomes being sequenced by NGS that do not have a genetic or physical map.computational genomics | comparative genomics | bioinformatics | chromosome breakpoints | mammals

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Section: Methodsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Reference-assisted chromosome assembly

Kim

Larkin

Cai

et al. 2013

Proc. Natl. Acad. Sci. U.S.A.

Self Cite

117

136

View full text Add to dashboard Cite

show abstract

“…In this paper, we have corrected an algorithm for isometric gene tree reconciliation, first presented by Ma et al [1,2] in the context of reconstruction of evolutionary histories in the infinite sites model. We have also improved the running time of the algorithm from O(N 2 ) to O(N log N ), where N is the total size of the two input trees.…”

Section: Discussionmentioning

confidence: 99%

“…The two papers by Ma et al [1,2] include the same algorithm for isometric gene tree reconciliation in the case when the input gene tree G I is unrooted and the species tree S I is rooted. In this section, we describe some of its details and point out mistakes in the original paper.…”

Section: Problems In the Original Algorithmmentioning

confidence: 99%

Isometric Gene Tree Reconciliation Revisited

Brejová

Gafurov

Pardubská

et al. 2016

Lecture Notes in Computer Science

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Background: Isometric gene tree reconciliation is a gene tree/species tree reconciliation problem where both the gene tree and the species tree include branch lengths, and these branch lengths must be respected by the reconciliation. The problem was introduced by in the context of reconstructing evolutionary histories of genomes in the infinite sites model. Results:In this paper, we show that the original algorithm by Ma et al. is incorrect, and we propose a modified algorithm that addresses the problems that we discovered. We have also improved the running time from O(N 2 ) to O(N log N), where N is the total number of nodes in the two input trees. Finally, we examine two new variants of the problem: reconciliation of two unrooted trees and scaling of branch lengths of the gene tree during reconciliation of two rooted trees. Conclusions:We provide several new algorithms for isometric reconciliation of trees. Some questions in this area remain open; most importantly extensions of the problem allowing for imprecise estimates of branch lengths.

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“…If gene families are described with reconciled trees with duplications, the software DupCAR [68] proposes the reconstruction of ancestral adjacencies. Nevertheless, its possible applications are rather limited as it does not handle losses and requires fully dated gene trees and species tree, in order to compute reconciliations that are compatible with the provided date information.…”

Section: Evolution Of Whole Genome With Adjacency Modelsmentioning

confidence: 99%

Duplication, Rearrangement and Reconciliation: A Follow-Up 13 Years Later

Chauve

El-Mabrouk

Guéguen

et al. 2013

Computational Biology

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Abstract. The evolution of genomes can be studied at at least three different scales: the nucleotide level, accounting for substitutions and indels, the gene level, accounting for gains and losses, and the genome level, accounting for rearrangements of chromosome organization. While the nucleotide and gene levels are now often integrated in a single model using reconciled gene trees, very little work integrates the genome level as well, and considers gene trees and gene orders simultaneously. In a seminal book chapter published in 2000 and entitled "Duplication, Rearrangement and Reconciliation", Sankoff and El-Mabrouk outlined a general approach, making a step in that direction. This avenue has been poorly exploited by the community for over ten years, but recent developments allow the design of integrated methods where phylogeny informs the study of synteny and vice-versa. We review these developments and show how this influence of synteny on gene tree construction can be implemented.

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DUPCAR: Reconstructing Contiguous Ancestral Regions with Duplications

Cited by 54 publications

References 33 publications

Reference-assisted chromosome assembly

Reference-assisted chromosome assembly

Isometric Gene Tree Reconciliation Revisited

Duplication, Rearrangement and Reconciliation: A Follow-Up 13 Years Later

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