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COMPUTING THE ASSIGNMENT OF ORTHOLOGOUS GENES VIA GENOME REARRANGEMENT
2005
Proceedings of the 3rd Asia-Pacific Bioinformatics Conference
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This makes the assignment of orthologous genes via genome rearrangement a very promising approach. ...
Our preliminary experiments on simulated and real data have demonstrated that ortholog assignment via genome rearrangement is a very promising method. ...
doi:10.1142/9781860947322_0037
fatcat:anppmueskzc7xjofjn2wj65tiy
MSOAR: A High-Throughput Ortholog Assignment System Based on Genome Rearrangement
2007
Journal of Computational Biology
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The assignment of orthologous genes between a pair of genomes is a fundamental and challenging problem in comparative genomics, since many computational methods for solving various biological problems ...
In this framework, orthologous genes are assumed to correspond to each other in the most parsimonious evolutionary scenario involving both genome rearrangement and (post-speciation) gene duplication. ...
Also, the authors wish it to be known that the first two authors should be regarded as joint First Authors of this paper. ...
doi:10.1089/cmb.2007.0048
pmid:17990975
fatcat:q6pso2acsvfdxbjh2ymoodrg3i
A Parsimony Approach to Genome-Wide Ortholog Assignment
[chapter]
2006
Lecture Notes in Computer Science
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The assignment of orthologous genes between a pair of genomes is a fundamental and challenging problem in comparative genomics, since many computational methods for solving various biological problems ...
In this framework, orthologous genes are assumed to correspond to each other in the most parsimonious evolutionary scenario involving both genome rearrangement and (post-speciation) gene duplication. ...
Also, the authors wish it to be known that the first two authors should be regarded as joint First Authors of this paper. The contact email addresses are {zfu,jiang}@cs.ucr.edu ...
doi:10.1007/11732990_47
fatcat:nzrcygpnfzeyrb2czkz3ef6afm
Some Algorithmic Challenges in Genome-Wide Ortholog Assignment
2010
Journal of Computer Science and Technology
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Genome-scale assignment of orthologous genes is a fundamental and challenging problem in computational biology and has a wide range of applications in comparative genomics, functional genomics, and systems ...
genome into another by the smallest number of genome rearrangement events including reversal, translocation, fusion, and fission, as well as gene duplication events. ...
Parsimony Approach to Ortholog Assignment via Genome Rearrangement Here, we give more details of the parsimony approach that we recently introduced in [8-10] for assigning orthologs between two closely ...
doi:10.1007/s11390-010-9304-6
fatcat:tx2q42pgafgh3c53i5x5bzix6m
Assignment of Orthologous Genes via Genome Rearrangement
2005
IEEE/ACM Transactions on Computational Biology & Bioinformatics
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The assignment of orthologous genes between a pair of genomes is a fundamental and challenging problem in comparative genomics. ...
First, the problem is formulated as that of computing the signed reversal distance with duplicates between the two genomes of interest. ...
Acknowledgments We thank the anonymous referees for many valuable comments and several useful references. ...
doi:10.1109/tcbb.2005.48
pmid:17044168
fatcat:vqqt3fu7drbypmxgs6b6ncfk44
DODO: an efficient orthologous genes assignment tool based on domain architectures. Domain based ortholog detection
2010
BMC Bioinformatics
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With rapidly increasing number of sequenced genomes, constructing or updating ortholog relationship between all genomes requires lots of effort and computation time. ...
Orthologs are genes derived from the same ancestor gene loci after speciation events. Orthologous proteins usually have similar sequences and perform comparable biological functions. ...
This article has been published as part of BMC Bioinformatics Volume 11 Supplement 7, 2010 ...
doi:10.1186/1471-2105-11-s7-s6
fatcat:het6rof3lnbirkdmvcrqhsarje
Comparative Phylogenomics of Pathogenic and Non-Pathogenic Mycobacterium
2013
PLoS ONE
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In this work, we report the comparison of pathogenic and non-pathogenic Mycobacterium genomes. Phylogenetic trees were constructed using sequence of core orthologs, gene content and gene order. ...
It is found that while rearrangements between some Mycobacterium genomes are local within synteny blocks, few possess global rearrangements across the genomes. ...
Percentage micro-rearrangements between any two genomes was computed based on the difference in the number of reversals for all the core orthologs considered separately and the number of reversals computed ...
doi:10.1371/journal.pone.0071248
pmid:24015186
pmcid:PMC3756022
fatcat:ib27nyi56zhtle2vywo45wdgda
Orthology Detection Combining Clustering and Synteny for Very Large Datasets
2014
PLoS ONE
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The elucidation of orthology relationships is an important step both in gene function prediction as well as towards understanding patterns of sequence evolution. ...
Orthology assignments are usually derived directly from sequence similarities for large data because more exact approaches exhibit too high computational costs. ...
Acknowledgments We are thankful with Chunfang Zheng for providing us her scripts and guidance for genome rearrangements.
Author Contributions ...
doi:10.1371/journal.pone.0105015
pmid:25137074
pmcid:PMC4138177
fatcat:7rihs3rfk5hmbod7vhbdmztqhy
3D genome evolution and reorganization in the Drosophila melanogaster species group
2020
PLoS Genetics
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We find that the majority of TADs have been reorganized since the common ancestor of D. melanogaster and D. triauraria, via a combination of chromosomal rearrangements and gain/loss of TAD boundaries. ...
TAD reorganization between these two species is associated with a localized effect on gene expression, near the site of disruption. ...
Acknowledgments The authors acknowledge the Office of Advanced Research Computing (OARC) at Rutgers, The State University of New Jersey for providing access to the Amarel cluster and associated research ...
doi:10.1371/journal.pgen.1009229
pmid:33284803
fatcat:bc5vzsmqqvdn3nz3rhdwciilny
Descendants of Whole Genome Duplication within Gene Order Phylogeny
2008
Journal of Computational Biology
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Genome rearrangement phylogenetics requires that all genomes analyzed have the same set of orthologs, so that it is not possible to include doubled and unduplicated genomes in the same phylogeny. ...
for integrating genomic distance, halving and rearrangement median algorithms. ...
related genome, there is no question of which of the two paralogs of a gene in the former is the true ortholog of the corresponding single gene in the latter: the two paralogs have precisely the same ...
doi:10.1089/cmb.2008.0118
pmid:18788908
fatcat:224owa6tmjgntang32ps3p7jvi
MultiMSOAR 2.0: An Accurate Tool to Identify Ortholog Groups among Multiple Genomes
2011
PLoS ONE
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Based on a recently developed accurate tool, called MSOAR 2.0, for ortholog assignment between a pair of closely related genomes based on genome rearrangement, we present a new system MultiMSOAR 2.0, to ...
The identification of orthologous genes shared by multiple genomes plays an important role in evolutionary studies and gene functional analyses. ...
Acknowledgments We would like to thank Liqing Zhang for many constructive discussions, and the anonymous reviewer for many valuable suggestions.
Author Contributions ...
doi:10.1371/journal.pone.0020892
pmid:21712981
pmcid:PMC3119667
fatcat:l5oeiua3mrh2xa7suwoobethda
OrthoGNC: A Software for Accurate Identification of Orthologs Based on Gene Neighborhood Conservation
2017
Genomics, Proteomics & Bioinformatics
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Various genomic events, such as duplication and horizontal gene transfer, can cause erroneous assignment of orthology relations. ...
In addition to orthology detection, OrthoGNC can be employed to investigate the conservation of genomic context among potential orthologs detected by other methods. ...
Due to genome rearrangements, as well as gene gains/losses, genomic context is less conserved beyond the genus level. Nonetheless, it can be a strong evidence of orthology when found. ...
doi:10.1016/j.gpb.2017.07.002
pmid:29133277
pmcid:PMC5828658
fatcat:3uycotjyxzaynotj6lod55pq2a
Techniques for multi-genome synteny analysis to overcome assembly limitations
2006
Genome Informatics Series
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Genome scale synteny analysis, the analysis of relative gene-order conservation between species, can provide key insights into evolutionary chromosomal dynamics, rearrangement rates between species, and ...
One of the primary challenges facing multi-genome syntenic analysis is the uncertainty posed by genome assembly data with un-sequenced gaps and possible assembly errors. ...
), Bio-Molecular Engineering Research Center (BMERC Boston University) computing and support sta, Harvard's Center for Genomic Research (CGR) computing sta, and the y research community. ...
pmid:17503388
fatcat:au65i3w2qjbptlgzdjbmjkgozy
Homoeologs: What Are They and How Do We Infer Them?
2016
Trends in Plant Science
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In the second part, we survey experimental and computational methods of homoeolog inference, considering the strengths and limitations of each approach. ...
Here we review the definition of homoeology in historical and modern contexts and propose a precise and testable definition highlighting the connection between homoeologs and orthologs. ...
Acknowledgments The authors thank Evelyne Caestecker, Frédéric Choulet, Matthew Hannah, Ken Heyndrickx, Scott Jackson, John Jacobs, and Pieter Ouwerkerk for their feedback and discussion on the manuscript ...
doi:10.1016/j.tplants.2016.02.005
pmid:27021699
pmcid:PMC4920642
fatcat:wszcrgjz2bfdnkxzmzarme337y
Micro-evolution of three Streptococcus species: selection, antigenic variation, and horizontal gene inflow
2019
BMC Evolutionary Biology
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Genome sequencing of multiple Streptococcus strains demonstrated high variability in gene content and order even in closely related strains of the same species and created a newly emerged object for genomic ...
analysis, the pan-genome. ...
Funding The study was supported by the Russian Foundation of Basic Research under grant 16-54-21004 and program "Molecular and Cellular Biology" of the Russian Academy of Sciences. ...
doi:10.1186/s12862-019-1403-6
pmid:30917781
pmcid:PMC6437910
fatcat:vnypevi66rga3mqpoqykpieew4
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