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The SGN comparative map viewer
2008
Bioinformatics
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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
2005
Plant Physiology
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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
2010
BMC Bioinformatics
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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
2009
Nature Precedings
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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
2014
Nucleic Acids Research
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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
2014
PLoS ONE
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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
2009
Bioinformatics
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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
2018
Database: The Journal of Biological Databases and Curation
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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
2010
Database: The Journal of Biological Databases and Curation
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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]
2014
The Role of Bioinformatics in Agriculture
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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
2012
Agronomy
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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
2009
Journal of the Japanese Society for Horticultural Science
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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
2007
Plant Biotechnology
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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
2010
Nucleic Acids Research
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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
2008
Plant Physiology
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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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