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COMPUTING THE ASSIGNMENT OF ORTHOLOGOUS GENES VIA GENOME REARRANGEMENT

X. CHEN, J. ZHENG, Z. FU, P. NAN, Y. ZHONG, S. LONARDI, T. JIANG
2005 Proceedings of the 3rd Asia-Pacific Bioinformatics Conference  
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

Zheng Fu, Xin Chen, Vladimir Vacic, Peng Nan, Yang Zhong, Tao Jiang
2007 Journal of Computational Biology  
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]

Zheng Fu, Xin Chen, Vladimir Vacic, Peng Nan, Yang Zhong, Tao Jiang
2006 Lecture Notes in Computer Science  
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

Tao Jiang
2010 Journal of Computer Science and Technology  
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

Xin Chen, Jie Zheng, Zheng Fu, Peng Nan, Yang Zhong, S. Lonardi, Tao Jiang
2005 IEEE/ACM Transactions on Computational Biology & Bioinformatics  
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

Ting-wen Chen, Timothy H Wu, Wailap V Ng, Wen-chang Lin
2010 BMC Bioinformatics  
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

Arun N. Prasanna, Sarika Mehra, Jingfa Xiao
2013 PLoS ONE  
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

Marcus Lechner, Maribel Hernandez-Rosales, Daniel Doerr, Nicolas Wieseke, Annelyse Thévenin, Jens Stoye, Roland K. Hartmann, Sonja J. Prohaska, Peter F. Stadler, Christos A. Ouzounis
2014 PLoS ONE  
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

Nicole S. Torosin, Aparna Anand, Tirupathi Rao Golla, Weihuan Cao, Christopher E. Ellison, Bret Payseur
2020 PLoS Genetics  
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

Chunfang Zheng, Qian Zhu, David Sankoff
2008 Journal of Computational Biology  
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

Guanqun Shi, Meng-Chih Peng, Tao Jiang, Stein Aerts
2011 PLoS ONE  
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

Soheil Jahangiri-Tazehkand, Limsoon Wong, Changiz Eslahchi
2017 Genomics, Proteomics & Bioinformatics  
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

Arjun Bhutkar, Susan Russo, Temple F Smith, William M Gelbart
2006 Genome Informatics Series  
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?

Natasha M. Glover, Henning Redestig, Christophe Dessimoz
2016 Trends in Plant Science  
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

Pavel V. Shelyakin, Olga O. Bochkareva, Anna A. Karan, Mikhail S. Gelfand
2019 BMC Evolutionary Biology  
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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