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The SGN comparative map viewer

L. A. Mueller, A. A. Mills, B. Skwarecki, R. M. Buels, N. Menda, S. D. Tanksley
2008 Bioinformatics  
In addition to viewing and comparing different maps stored in the SGN database, the viewer allows users to upload their own maps and compare them to other maps in the system.  ...  Here we describe a web-based comparative viewer for mapping data, including genetic, physical and cytological maps, that is part of the SGN website (http://sgn.cornell.edu/) but that can also be installed  ...  SGN is supported by the NSF (DBI-0421634) and the USDA #2007-02777.  ... 
doi:10.1093/bioinformatics/btm597 pmid:18202028 fatcat:l7cpv5cp5zgsxp47bif5czrste

The SOL Genomics Network. A Comparative Resource for Solanaceae Biology and Beyond

L. A. Mueller
2005 Plant Physiology  
The SOL Genomics Network (SGN; http://sgn.cornell.edu) is a rapidly evolving comparative resource for the plants of the Solanaceae family, which includes important crop and model plants such as potato  ...  The aim of SGN is to relate these species to one another using a comparative genomics approach and to tie them to the other dicots through the fully sequenced genome of Arabidopsis (Arabidopsis thaliana  ...  The SGN Comparative Viewer.  ... 
doi:10.1104/pp.105.060707 pmid:16010005 pmcid:PMC1176404 fatcat:ddrcgjebnrhovbugeldlyeu2ae

solQTL: a tool for QTL analysis, visualization and linking to genomes at SGN database

Isaak Y Tecle, Naama Menda, Robert M Buels, Esther van der Knaap, Lukas A Mueller
2010 BMC Bioinformatics  
and algorithms for online visualization and cross-referencing of QTLs to relevant datasets and tools such as the SGN Comparative Map Viewer and Genome Browser.  ...  The new QTL module, solQTL, http://solgenomics.net/qtl/, employs a user-friendly web interface for uploading raw phenotype and genotype data to the database, R/QTL mapping software for on-the-fly QTL analysis  ...  Acknowledgements The project was funded by the USDA CSREES.  ... 
doi:10.1186/1471-2105-11-525 pmid:20964836 pmcid:PMC2984588 fatcat:76jqq2e56bgxzjhj56keb55hgu

SGN Database: From QTLs to Genomes

Isaak Tecle, Naama Menda, Robert Buels, Lukas Mueller
2009 Nature Precedings  
Using the Comparative Map Viewer, one can compare QTL map locations (A, B) to a variety of Solanaceae genetic maps (C) and tomato physical maps (D, E) including FingerPrint Contigs (FPC), Accessioned  ...  QTL and Comparative Map Analysis Phenotype and Genotype Data Analysis SGN code and software ftp://ftp.sgn.cornell.edu Phenotype and genotype raw data for upload to SGN Isaak Y Tecle, Naama Menda, Robert  ... 
doi:10.1038/npre.2009.3160.1 fatcat:ikbes2om2nh5zht3umthpcaswi

The Sol Genomics Network (SGN)—from genotype to phenotype to breeding

Noe Fernandez-Pozo, Naama Menda, Jeremy D. Edwards, Surya Saha, Isaak Y. Tecle, Susan R. Strickler, Aureliano Bombarely, Thomas Fisher-York, Anuradha Pujar, Hartmut Foerster, Aimin Yan, Lukas A. Mueller
2014 Nucleic Acids Research  
Tools such as BLAST, GBrowse and JBrowse for browsing genomes, expression and map data viewers, a locus community annotation system and a QTL analysis tools are available.  ...  The Sol Genomics Network (SGN, http: //solgenomics.net) is a web portal with genomic and phenotypic data, and analysis tools for the Solanaceae family and close relatives.  ...  Another feature of the SGN system is its support for multiple species, with the comparative viewer, an SGN custom application (9) .  ... 
doi:10.1093/nar/gku1195 pmid:25428362 pmcid:PMC4383978 fatcat:524lfl7zyba6vnfjuxiyw364o4

Tomato Genomic Resources Database: An Integrated Repository of Useful Tomato Genomic Information for Basic and Applied Research

B. Venkata Suresh, Riti Roy, Kamlesh Sahu, Gopal Misra, Debasis Chattopadhyay, Tongming Yin
2014 PLoS ONE  
TGRD is a user-friendly web-accessible relational database and uses CMAP viewer for graphical scanning of all the features.  ...  Tomato Genomic Resources Database (TGRD) allows interactive browsing of tomato genes, micro RNAs, simple sequence repeats (SSRs), important quantitative trait loci and Tomato-EXPEN 2000 genetic map altogether  ...  Acknowledgments Acknowledgement is due to the Director, National Institute of Plant Genome Research, New Delhi, India (NIPGR) for providing facilities.  ... 
doi:10.1371/journal.pone.0086387 pmid:24466070 pmcid:PMC3897720 fatcat:jjbfg3nscvcytjxykxu3d3cpfu

CMap 1.01: a comparative mapping application for the Internet

K. Youens-Clark, B. Faga, I. V. Yap, L. Stein, D. Ware
2009 Bioinformatics  
CMap is a web-based tool for displaying and comparing maps of any type and from any species.  ...  A user can compare an unlimited number of maps, view pair-wise comparisons of known correspondences, and search for maps or for features by name, species, type and accession.  ...  genome viewer (Krzywinski et al., 2009) .  ... 
doi:10.1093/bioinformatics/btp458 pmid:19648141 pmcid:PMC2773250 fatcat:tfsvqfmtzjdh3dtimb6gap5u74

A comparative synteny analysis tool for target-gene SNP marker discovery: connecting genomics data to breeding in Solanaceae

Junkyoung Choe, Ji-Eun Kim, Bong-Woo Lee, Jeong Hee Lee, Moon Nam, Youn-Il Park, Sung-Hwan Jo
2018 Database: The Journal of Biological Databases and Curation  
We developed a comparative analysis tool and web-based genome viewer to identify orthologous genes based synteny as well as sequence similarity between tomato, pepper and potato.  ...  Furthermore, it provides access to single nucleotide-polymorphism markers from the massive genetic resource pool in order to accelerate the development of molecular markers for candidate orthologs in the  ...  For instance, the Sol Genomics Network (SGN) developed a comparative viewer that visualizes different types of maps and markers in Solanaceae species (13, 14) .  ... 
doi:10.1093/database/bay047 pmid:29873704 pmcid:PMC6007222 fatcat:eiq3plepgzd5dj37qbxsfv5tni

Choosing a genome browser for a Model Organism Database: surveying the Maize community

Taner Z. Sen, Lisa C. Harper, Mary L. Schaeffer, Carson M. Andorf, Trent E. Seigfried, Darwin A. Campbell, Carolyn J. Lawrence
2010 Database: The Journal of Biological Databases and Curation  
We thank the anonymous reviewers whose suggestions helped us improve this article. We very much appreciate the useful comments by Dr Patrick Armstrong.  ...  we could not have created an implementation of the MaizeGDB Genome Browser customized to support our users' needs.  ...  GBrowse can also be integrated with the comparative map viewer CMAP (35), the BioMart data mining system (36) and the TextPresso text mining tool (37) .  ... 
doi:10.1093/database/baq007 pmid:20627860 pmcid:PMC2911842 fatcat:6ihbvxcmdnfypo2clanjfma5vq

Genomic Databases for Crop Improvement [chapter]

Kaitao Lai, MICHA_ Lorenc, David Edwards
2014 The Role of Bioinformatics in Agriculture  
In this review, we outline some of the features of plant genome databases, identify specific resources for the improvement of individual crops and comment on the potential future direction of crop genome  ...  Translating the vast abundance of data being produced by genome technologies requires the development of custom bioinformatics tools and advanced databases.  ...  Acknowledgments The authors would like to acknowledge funding support from the Grains Research and Development Corporation (Project DAN00117) and the Australian Research Council (Projects LP0882095, LP0883462  ... 
doi:10.1201/b16568-9 fatcat:y2eht5etmrfwdbxbcxusinkcxu

Genomic Databases for Crop Improvement

Kaitao Lai, Michał T. Lorenc, David Edwards
2012 Agronomy  
In this review, we outline some of the features of plant genome databases, identify specific resources for the improvement of individual crops and comment on the potential future direction of crop genome  ...  Translating the vast abundance of data being produced by genome technologies requires the development of custom bioinformatics tools and advanced databases.  ...  Acknowledgments The authors would like to acknowledge funding support from the Grains Research and Development Corporation (Project DAN00117) and the Australian Research Council (Projects LP0882095, LP0883462  ... 
doi:10.3390/agronomy2010062 fatcat:povutl3wufhhje5ovsocnr26ju

Web Databases for Omics Data in Tomato

Ayako Suzuki, Keita Suwabe, Kentaro Yano
2009 Journal of the Japanese Society for Horticultural Science  
In addition, the number of genome sequences and expression sequence tags in the International Nucleotide Sequence Databases has been rapidly increasing.  ...  Tomato (Solanum lycopersicum) is a model plant of the Solanaceae family.  ...  Acknowledgements This work was supported in part by a Grant-in-Aid for Scientific Research (B) (20380022) to KY from the Japan Society for the Promotion of Science (JSPS).  ... 
doi:10.2503/jjshs1.78.23 fatcat:dk6ypwleazcundbewuyghtyoni

Genomic Databases for Tomato

Kentaro Yano, Koh Aoki, Daisuke Shibata
2007 Plant Biotechnology  
SGN and NCBI provide map viewers that show relationships between the different linkage maps. Bacterial artificial chromosomes and physical maps SGN provides BAC information, including physical maps.  ...  SGN also provides information on the use of fluorescence in-situ hybridization (FISH) mapping to verify the linkage and physical maps.  ... 
doi:10.5511/plantbiotechnology.24.17 fatcat:vq4sw32p6neg5a6recvyuxwmeu

The Sol Genomics Network (solgenomics.net): growing tomatoes using Perl

A. Bombarely, N. Menda, I. Y. Tecle, R. M. Buels, S. Strickler, T. Fischer-York, A. Pujar, J. Leto, J. Gosselin, L. A. Mueller
2010 Nucleic Acids Research  
SGN hosts several genome maps and sequences, including a pre-release of the tomato (Solanum lycopersicum cv Heinz 1706) reference genome.  ...  The database architecture combines SGN-specific schemas and the community-developed Chado schema (http://gmod.org/wiki/Chado) for compatibility with other genome databases.  ...  And also would like to gratefully acknowledge the National Science Foundation (NSF) and the United States Department of Agriculture (USDA) and ATC Inc. for funding of SGN.  ... 
doi:10.1093/nar/gkq866 pmid:20935049 pmcid:PMC3013765 fatcat:pecgrrxhujcidenzoz2jcue3yq

A Community-Based Annotation Framework for Linking Solanaceae Genomes with Phenomes

N. Menda, R. M. Buels, I. Tecle, L. A. Mueller
2008 Plant Physiology  
The SOL Genomics Network (SGN; http://www.sgn.cornell.edu) is a clade-oriented database (COD), which provides a more scalable and comparative framework for biological information.  ...  Here we describe the background, features, implementation, results, and development road map of SGN's community annotation tools for curating genotypes and phenotypes.  ...  for contributing to the development of the Solanaceae Phenotype Ontology.  ... 
doi:10.1104/pp.108.119560 pmid:18539779 pmcid:PMC2492603 fatcat:idtk3vqar5he7j5756socytbiy
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