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CARTHAGENE: constructing and joining maximum likelihood genetic maps

T Schiex, C Gaspin
1997 Proceedings. International Conference on Intelligent Systems for Molecular Biology  
This paper presents a new approach to two important problems in genetic mapping: automatically ordering markers to obtain a multipoint maximum likelihood map and building a multipoint maximum likelihood  ...  The approach has been used to build joined maps for the wasp Trichogramma brassicae and on random pooled data sets.  ...  Its ability to tackle data sets with a large number of missing allows the construction of multipoint maximum likelihood joined maps with an apparently better probability of success than the package JOINMAP  ... 
pmid:9322047 fatcat:fdknv3uvvzcjzfulm4p7o6u3du

Page 2527 of Genetics Vol. 176, Issue 4 [page]

2007 Genetics  
Gaspin, 1997 CarthaGéne: constructing and join- ing maximum likelihood genetic maps. Proceedings of Intelligent Systems of Molecular Biology °97, June 1997, Halkidiki, Greece.  ...  GIANOLA, 2002 A Bayesian ap- proach for constructing genetic maps when markers are mis- coded. Genet. Sel. Evol. 34: 353-369. Construction of multilocus Acad. Sci. USA 2527 Scutex, T., and C.  ... 

Page 64 of Animal Genetics Vol. 35, Issue 1 [page]

2004 Animal Genetics  
Genetics, selection, evolution 34, 521-33. Schiex T. & Gaspin C. (1997) CARTHAGENE: constructing and joining maximum likelihood genetic maps.  ...  Cytogenetics and Cell Genetics 82, 182-8. © 2004 International Society for Animal Genetics, Animal Genetics, 35, 63-65  ... 

Multipoint-likelihood maximization mapping on 4 segregating populations to achieve an integrated framework map for QTL analysis in pot azalea (Rhododendron simsii hybrids)

Ellen De Keyser, Qing Shu, Erik Van Bockstaele, Jan De Riek
2010 BMC Molecular Biology  
A combination of regression mapping (JoinMap) and multipoint-likelihood maximization (Carthagène) enabled the construction of 4 maps and their alignment.  ...  For this purpose, QTL mapping in diverse genetic backgrounds appeared to be a must and therefore 4 mapping populations were made and analyzed.  ...  Additional file 5: Individual map lengths. Table that gives an overview of the length of the individual optimized and framework maps, in total and per linkage group.  ... 
doi:10.1186/1471-2199-11-1 pmid:20070894 pmcid:PMC2837023 fatcat:hlnvmixzobad3lmpc3gzw2oqqm

Page 283 of Genetics Vol. 169, Issue 1 [page]

2005 Genetics  
Gaspin, 1997 Carthagene: constructing and join- ing maximum likelihood genetic maps. Proc. Int. Conf. Intell. Syst. Mol. Biol. 5: 258-267. SPELMAN, R. J., W. Copprerers, L. Karim, J. A. M.  ...  ., 2001 Construction and characterization of a bovine BAC library with four genome-equivalent coverage. Genet. Sel. Evol. 33: 543-548 Ewinc, B., L. Hiniier, M. C. WeNp.L and P.  ... 

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  ...  This radiation hybrid map has the highest resolution of any porcine map to date and its integration with the porcine linkage map (reported here) will greatly facilitate the positional cloning of genes  ...  Acknowledgments This work was supported in part by USDA/NRI-CSREES Grant AG2001-35205-11698 and USDA-ARS AG58-5438-2-313.  ... 
doi:10.1016/j.ygeno.2005.04.010 pmid:16246521 fatcat:vevwep2dazczpcpoxi4recxiyq

Page 262 of Genetics Vol. 167, Issue 1 [page]

2004 Genetics  
Gaspin, 1997 CARTHAGENE: constructing and joining maximum likelihood gene maps. Proc. Int. Conf. Intell. Svst. Mol. Biol. 5: 258-267 Scuuc, M. D., C. M. Hutrer, A. VETTERSTRAND, M. S. GAUDETTE, Tr.  ...  Genetics 167: 243-252. Beeman, R. W., and S. J. Brown, 1999 RAPD-based genetic linkage map of Tribolium castaneum. Genetics 153: 333-338. Beye, M., and R. F. A.  ... 

Page 510 of Genetics Vol. 178, Issue 1 [page]

2008 Genetics  
Gaspin, 1997 CARTHAGENE: constructing and joining maximum likelihood gene maps. Proc. Int. Conf. Intell. Syst. Mol. Biol. 5: 258-267. ScHON, C. C., H. F. Urz, S. Gron, B. TRUBERG, S.  ...  ToLopko et al., 2004 Comparative map and trait viewer (CMTV): an integrated bioinformatic tool to construct consensus maps and compare QTL and functional genomics data across ge- nomes and experiments.  ... 

An integrated genetic and cytogenetic map for the Mediterranean fruit fly, Ceratitis capitata, based on microsatellite and morphological markers

Elias E. Stratikopoulos, Antonios A. Augustinos, Yannis G. Petalas, Michael N. Vrahatis, Anastasios Mintzas, Konstantinos D. Mathiopoulos, Antigone Zacharopoulou
2007 Genetica  
The construction of an integrated map covering the whole genome should greatly facilitate genetic studies and future genome sequence projects of the species.  ...  A genetic map based on microsatellite polymorphisms and visible mutations of the Mediterranean fruit fly (medfly), Ceratitis capitata is presented.  ...  Papaggeli and K.Oikonomou for support in genotyping and in situ hybridization and G. Franz and J. Cladera for providing medfly strains. E. E.  ... 
doi:10.1007/s10709-007-9195-9 pmid:17786564 fatcat:m74osz2f7vganhlcdctggg2jau

Lep-MAP: fast and accurate linkage map construction for large SNP datasets

Pasi Rastas, Lars Paulin, Ilkka Hanski, Rainer Lehtonen, Petri Auvinen
2013 Computer applications in the biosciences : CABIOS  
We demonstrate that Lep-MAP outperforms other methods on real and simulated data. We construct a genome-wide linkage map of the Glanville fritillary butterfly (Melitaea cinxia) with over 40 000 SNPs.  ...  Results: We describe a novel tool, called Lepidoptera-MAP (Lep-MAP), for constructing accurate linkage maps with ultradense genome-wide SNP data.  ...  Suvi Ikonen, Annukka Ruokolainen and Suvi Saarnio are thanked for rearing the butterflies and preparing samples for genotyping.  ... 
doi:10.1093/bioinformatics/btt563 pmid:24078685 pmcid:PMC4433499 fatcat:5yj7bqjjevaxzmpuahvurgwysu

Developing market class specific InDel markers from next generation sequence data in Phaseolus vulgaris L

Samira Mafi Moghaddam, Qijian Song, Sujan Mamidi, Jeremy Schmutz, Rian Lee, Perry Cregan, Juan M. Osorno, Phillip E. McClean
2014 Frontiers in Plant Science  
To highlight their usefulness, they were employed to construct a phylogenetic tree and a genetic map, showing that InDel markers are reliable, simple, and accurate.  ...  Next generation sequence data provides valuable information and tools for genetic and genomic research and offers new insights useful for marker development.  ...  The availability of high density markers affects the success of genetic map construction, map-based cloning (Pacurar et al., 2012) and diversity studies.  ... 
doi:10.3389/fpls.2014.00185 pmid:24860578 pmcid:PMC4026720 fatcat:hsgp5eozmrcf7akx5gadt7knvy

A high-resolution radiation hybrid map of rhesus macaque chromosome 5 identifies rearrangements in the genome assembly

Genesio M. Karere, Lutz Froenicke, Lee Millon, James E. Womack, Leslie A. Lyons
2008 Genomics  
A 10,000-rad radiation hybrid (RH) cell panel of the rhesus macaque was generated to construct a comprehensive RH map of chromosome 5. The map represents 218 markers typed in 185 RH clones.  ...  Alignments of the RH map to macaque and human genome sequences confirm a large inversion and reveal a previously unreported telomeric inversion.  ...  We thank Elaine Owens (Texas A and M University) for technical support in generating the hybrid cells and Carolyn Erdman for reviewing the manuscript. Appendix A.  ... 
doi:10.1016/j.ygeno.2008.05.013 pmid:18601997 pmcid:PMC2605074 fatcat:i7fllhqgzvbmpppinwawpzrdrq

Computational approaches and software tools for genetic linkage map estimation in plants

J. Cheema, J. Dicks
2009 Briefings in Bioinformatics  
Here, we aim to give a flavour of computational approaches for genetic map estimation, discussing briefly many of the key concepts involved, and describing a selection of software tools that employ them  ...  This review is intended both for plant geneticists as an introduction to software tools with which to estimate genetic maps, and for bioinformaticians as an introduction to the underlying computational  ...  They would also like to thank David Garvin and John Snape for their valuable guidance on the practicalities of genetic map estimation.  ... 
doi:10.1093/bib/bbp045 pmid:19933208 fatcat:euc4pca6jrdlfoakjhu3wax7ve

Characterizing Uncertainty in High-Density Maps from Multiparental Populations

Daniel Ahfock, Ian Wood, Stuart Stephen, Colin R. Cavanagh, B. Emma Huang
2014 Genetics  
We derive the asymptotic joint distribution of maximum composite likelihood estimators for intermarker distances.  ...  Multiparental populations are of considerable interest in high-density genetic mapping due to their increased levels of polymorphism and recombination relative to biparental populations.  ...  Acknowledgments Many thanks to Andrew George and Hien Nguyen for helpful discussions and comments. Daniel Ahfock was supported by  ... 
doi:10.1534/genetics.114.167577 pmid:25236453 pmcid:PMC4174924 fatcat:ikeypegdbvdvzcewfiyv5cb2oe

A 12,000-rad porcine radiation hybrid (IMNpRH2) panel refines the conserved synteny between SSC12 and HSA17

Wan-Sheng Liu, Katie Eyer, Hiroshi Yasue, Benjamin Roelofs, Hideki Hiraiwa, Takeshi Shimogiri, Earl Landrito, Joseph Ekstrand, Michael Treat, Anette Rink, Martine Yerle, Denis Milan (+1 others)
2005 Genomics  
The markers were ordered in 16 linkage groups at LOD 6.0 using framework markers previously mapped on the IMpRH 7000-rad SSC12 and porcine genetic maps.  ...  We report an initial, highresolution RH map of SSC12 on the 12,000-rad IMNpRH2 panel using CarthaGene software.  ...  Acknowledgments This work was supported by a grant from the USDA-CSREES (2004-35205-14244) to C.W.B. and the Program for the Promotion of Basic Research Activity for Innovative Biosciences of the Bio-oriented  ... 
doi:10.1016/j.ygeno.2005.08.006 pmid:16289748 fatcat:x5tu3qsbh5bj7camxu73v27yxi
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