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A comparative genome approach to marker ordering

T. Faraut, S. de Givry, P. Chabrier, T. Derrien, F. Galibert, C. Hitte, T. Schiex
2007 Bioinformatics  
We propose an algorithmic formalization of a genome comparison approach to marker ordering.  ...  In order to integrate a comparative mapping approach in the algorithmic process of map construction and selection, we extend the usual statistical model describing the experimental data, here radiation  ...  In order to test the efficiency of our method on a real example, we applied this comparative approach to the construction of a RH map of a whole canine chromosome (CFA2 - figure 4 ) using a set of 426  ... 
doi:10.1093/bioinformatics/btl321 pmid:17237105 fatcat:5mzpfdseubdsbkl7mls4tknlnq

A high resolution radiation hybrid map of bovine chromosome 14 identifies scaffold rearrangement in the latest bovine assembly

Elisa Marques, Simon de Givry, Paul Stothard, Brenda Murdoch, Zhiquan Wang, James Womack, Stephen S Moore
2007 BMC Genomics  
Conclusion: The increase of publicly available markers shifts the rate limiting step from marker discovery to the correct identification of their order for further use by the research community.  ...  This high resolution map of bovine chromosome 14 will facilitate identification of regions in the sequence assembly where additional information is required to resolve marker ordering.  ...  Acknowledgements This work was funded by Grant Number 2003A245R from Alberta Agriculture Research Institute, CDN-DairyGen/CRD 313675-04 and NSERC-CRD PJ313675-04 awarded to S.S. Moore.  ... 
doi:10.1186/1471-2164-8-254 pmid:17655763 pmcid:PMC1959194 fatcat:sm4feizmtba2jhrsnr6rvo2kqm

Constructing Consensus Genetic Maps in Comparative Analysis

Xin Chen, Jian-Yi Yang
2010 Journal of Computational Biology  
In this article, we propose a comparative approach to constructing consensus genetic maps for a genome, which further takes into account the order relations from a closely related genome when resolving  ...  Many computational approaches have been proposed on the basis of only the marker order relations provided by a given set of individual genetic maps.  ...  ACKNOWLEDGMENTS We would like to thank Dr.  ... 
doi:10.1089/cmb.2009.0268 pmid:20958247 fatcat:u3qd57dlcjbbtbu2hurk27m7de

Statistical confidence measures for genome maps: application to the validation of genome assemblies

Bertrand Servin, Simon de Givry, Thomas Faraut
2010 Computer applications in the biosciences : CABIOS  
Results: We propose new methods to derive statistical measures of confidence on genome maps using a comparative model for radiation hybrid data.  ...  However, current mapping approach lack statistical confidence measures necessary to identify precisely relevant inconsistencies between a genome map and an assembly.  ...  The authors are grateful to Christophe Hitte (CNRS-UMR6061) for kindly providing the dog RH dataset as a case study.  ... 
doi:10.1093/bioinformatics/btq598 pmid:21076149 fatcat:n5ck6v5rsngkbkghyfqkbpknzy

Genomics Approaches for Crop Improvement against Abiotic Stress

Bala Anı Akpınar, Stuart J. Lucas, Hikmet Budak
2013 The Scientific World Journal  
As traditional strategies for crop improvement approach their limits, the era of genomics research has arisen with new and promising perspectives in breeding improved varieties against abiotic stresses  ...  As sessile organisms, plants are inevitably exposed to one or a combination of stress factors every now and then throughout their growth and development.  ...  Comparative genomics has contributed significantly to the emergence of the "genome zipper" concept, which enables the determination of a virtual gene order in a partially sequenced genome.  ... 
doi:10.1155/2013/361921 pmid:23844392 pmcid:PMC3690750 fatcat:jd54rfszpza2znljgqdcjpyzji

Aspects of comparative genomics in the gilthead seabream, Sparusaurata

BRIDGEMAP Consortium, Georgios Kotoulas
2006 Israeli Journal of Aquaculture (Bamidgeh)  
Therefore, comparative genomics is increasingly applied as a shortcut to link sequence, syntenies, and gene order information, and function.  ...  An experimental shortcut to comparative mapping has been the use of cross species amplification of mapped microsatellite markers, an approach that may lead to comparative linkage maps.  ... 
doi:10.46989/001c.20454 fatcat:2ts2eg6g45h6bdpobgqtiqa46m

High resolution radiation hybrid maps of bovine chromosomes 19 and 29: comparison with the bovine genome sequence assembly

Aparna Prasad, Thomas Schiex, Stephanie McKay, Brenda Murdoch, Zhiquan Wang, James E Womack, Paul Stothard, Stephen S Moore
2007 BMC Genomics  
When aligned with the current bovine build 3.1, the order of markers on the RH map for BTA19 and 29 showed inconsistencies with respect to the genome assembly.  ...  High resolution radiation hybrid (RH) maps can facilitate genome sequence assembly by correctly ordering genes and genetic markers along chromosomes.  ...  Acknowledgements The authors gratefully acknowledge the early pre-publication access under the Fort Lauderdale conventions to the draft bovine genome sequence provided by the Baylor College of Medicine  ... 
doi:10.1186/1471-2164-8-310 pmid:17784962 pmcid:PMC2064936 fatcat:xfwfvj62avet3py5ttbs6vb3mi

Reversals of Fortune [chapter]

David Sankoff, Chungfang Zheng, Aleksander Lenert
2005 Lecture Notes in Computer Science  
We combine heuristics for the first two problems with an exact algorithm for the third to solve a moderate-sized instance comparing maps of cereal genomes.  ...  Three examples, all of which are hard: 1) Orientation assignment for unsigned genomes. 2 ) Ortholog identification in the presence of multiple copies of genes. 3) Linearisation of partially ordered genomes  ...  Thanks to Glenn Tesler for a discussion of strategies in his GRIMM software.  ... 
doi:10.1007/11554714_12 fatcat:4wfpjowmxfenxbjrfe7kmsgmgq

Measuring conservation of contiguous sets of autosomal markers on bovine and porcine genomes in relation to the map of the human genome

Zhihua Jiang, Jenna S Melville, Honghe Cao, Sudhir Kumar, Alan Filipski, Ann M Verrinder Gibbins
2002 Genome  
The relative linear locations of these genes on human sequence maps were used as "rulers" to annotate bovine and porcine genomes based on a CSAM (contiguous sets of autosomal markers) approach.  ...  The number of potential CSAMs for which no markers are currently available were estimated to be 63 between human and bovine genomes and 18 between human and porcine genomes.  ...  We are also grateful to anonymous reviewers for comments and advice on revising the manuscript.  ... 
doi:10.1139/g02-038 pmid:12175081 fatcat:yf2hc5jefjcwhnn4oorttwl5oq

Page 325 of Animal Genetics Vol. 30, Issue 5 [page]

1999 Animal Genetics  
A 5000 rad bovine whole-genome radiation hybrid panel was recently constructed in order to integrate existing cattle linkage maps with evolutionarily conserved genes and provide high resolution comparative  ...  To maximize the potential of this approach, it is necessary to develop iinear maps of Type I loci that establish boundaries of conserved gene order between species.  ... 

A whole-genome, radiation hybrid mapping resource of hexaploid wheat

Vijay K. Tiwari, Adam Heesacker, Oscar Riera-Lizarazu, Hilary Gunn, Shichen Wang, Yi Wang, Young Q. Gu, Etienne Paux, Dal-Hoe Koo, Ajay Kumar, Ming-Cheng Luo, Gerard Lazo (+7 others)
2016 The Plant Journal  
However, comparative genomics approaches are limited to syntenic inference and recombination is suppressed within the pericentromeric regions of wheat chromosomes, thus, precise ordering of physical maps  ...  In wheat, ordering of whole-genome or hierarchical shotgun sequencing contigs is primarily based on recombination and comparative genomics-based approaches.  ...  ACKNOWLEDGEMENTS This work was supported by funding from the National Science Foundation, Plant Genome Research Program (NSF-PGRP) grant no. IOS-082210.  ... 
doi:10.1111/tpj.13153 pmid:26945524 fatcat:zqc6nkun6nhdlan5lzw4svvzaa

Application of Population Sequencing (POPSEQ) for Ordering and Imputing Genotyping-by-Sequencing Markers in Hexaploid Wheat

Erena A. Edae, Robert L. Bowden, Jesse Poland
2015 G3: Genes, Genomes, Genetics  
For species with a reference genomic sequence, markers can be ordered on the physical map. However, in the absence of reference marker order, the use and imputation of GBS markers is challenging.  ...  Here, we demonstrate how the population sequencing (POPSEQ) approach can be used to provide marker context for GBS in wheat.  ...  However, many other imputation approaches that have been developed first require markers to be linearly ordered on a chromosome.  ... 
doi:10.1534/g3.115.020362 pmid:26530417 pmcid:PMC4683627 fatcat:6y6woanil5gsvl2qpdcjcx3wce

The genome of the medieval Black Death agent (extended abstract) [article]

Ashok Rajaraman and Eric Tannier and Cedric Chauve
2013 arXiv   pre-print
a comparative approach.  ...  We show that recent computational paleogenomics methods, aiming at reconstructing the organization of ancestral genomes from the comparison of extant genomes, can be used to correct, order and complete  ...  Acknowledgements This work was supported by NSERC Discovery Grant to C.C., a PIMS IGTC Fellowship to A.R. and ANR-10-BINF-01-01 Ancestrome to E.T.  ... 
arXiv:1307.7642v1 fatcat:qwyph37zmzhq5jfotc3priq55e

Piggy-BACing the human genome

Stacey N. Meyers, Margarita B. Rogatcheva, Denis M. Larkin, Martine Yerle, Denis Milan, Rachel J. Hawken, Lawrence B. Schook, Jonathan E. Beever
2005 Genomics  
Using the INRA -Minnesota porcine radiation hybrid panel, we have constructed a human -pig comparative map composed of 2274 loci, including 206 ESTs and 2068 BAC-end sequences, assigned to 34 linkage groups  ...  The average spacing between comparative anchor loci is 1.15 Mb based on human genome sequence coordinates. A total of 51 conserved synteny groups that include 173 conserved segments were identified.  ...  relief from these experimental limitations and allows for a more targeted approach to physical and comparative mapping.  ... 
doi:10.1016/j.ygeno.2005.04.010 pmid:16246521 fatcat:vevwep2dazczpcpoxi4recxiyq

Assessing mapping progress in the Human Genome Project

D. Cox, E. Green, E. Lander, D Cohen, R. Myers
1994 Science  
The ordering of bins within a cluster again involves a statistical procedure for comparing alternative orders.  ...  Describe the observed distribution of the number of markers per bin and compare it to the distribution expected for a randomly spaced collection of markers.  ... 
doi:10.1126/science.8091223 pmid:8091223 fatcat:ggerniizdnfb3irsyxxhznuoia
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