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ABSTRACT: Gramene is a well-established resource for plant comparative genome analysis. Data are generated through automated and curated analyses and made available through web interfaces such as GrameneMart. The Gramene project was an early adopter of the BioMart software, which remains an integral and well-used component of the Gramene website. BioMart accessible data sets include plant gene annotations, plant variation catalogues, genetic markers, physical mapping entities, public DNA/mRNA sequences of various types and curated quantitative trait loci for various species. DATABASE URL: http://www.gramene.org/biomart/martview.
Database The Journal of Biological Databases and Curation 01/2012; 2012:bar056. · 2.07 Impact Factor
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Ken Youens-Clark,
Edward S. Buckler,
Terry M. Casstevens,
Charles Chen,
Genevieve DeClerck,
Paul Derwent,
Palitha Dharmawardhana,
Pankaj Jaiswal,
Paul Kersey,
A. S. Karthikeyan,
Jerry Lu,
Susan McCouch,
Liya Ren,
William Spooner,
Joshua C. Stein,
Jim Thomason,
Sharon Wei,
Doreen Ware
Nucleic Acids Research. 01/2011; 39:1085-1094.
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Jonathan M Guberman,
J Ai,
O Arnaiz,
Joachim Baran,
Andrew Blake,
Richard Baldock,
Claude Chelala,
David Croft,
Anthony Cros,
Rosalind J Cutts, [......],
Jun Wang,
Jianxin Wang,
Brett Whitty,
D T Wong,
Marie Wong-Erasmus,
L Yao, Ken Youens-Clark,
Christina Yung,
Junjun Zhang,
Arek Kasprzyk
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ABSTRACT: BioMart Central Portal is a first of its kind, community-driven effort to provide unified access to dozens of biological databases spanning genomics, proteomics, model organisms, cancer data, ontology information and more. Anybody can contribute an independently maintained resource to the Central Portal, allowing it to be exposed to and shared with the research community, and linking it with the other resources in the portal. Users can take advantage of the common interface to quickly utilize different sources without learning a new system for each. The system also simplifies cross-database searches that might otherwise require several complicated steps. Several integrated tools streamline common tasks, such as converting between ID formats and retrieving sequences. The combination of a wide variety of databases, an easy-to-use interface, robust programmatic access and the array of tools make Central Portal a one-stop shop for biological data querying. Here, we describe the structure of Central Portal and show example queries to demonstrate its capabilities.
Database The Journal of Biological Databases and Curation 01/2011; 2011:bar041. · 2.07 Impact Factor
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Ken Youens-Clark,
Ed Buckler,
Terry Casstevens,
Charles Chen,
Genevieve Declerck,
Paul Derwent,
Palitha Dharmawardhana,
Pankaj Jaiswal,
Paul Kersey,
A S Karthikeyan,
Jerry Lu,
Susan R McCouch,
Liya Ren,
William Spooner,
Joshua C Stein,
Jim Thomason,
Sharon Wei,
Doreen Ware
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ABSTRACT: Now in its 10th year, the Gramene database (http://www.gramene.org) has grown from its primary focus on rice, the first fully-sequenced grass genome, to become a resource for major model and crop plants including Arabidopsis, Brachypodium, maize, sorghum, poplar and grape in addition to several species of rice. Gramene began with the addition of an Ensembl genome browser and has expanded in the last decade to become a robust resource for plant genomics hosting a wide array of data sets including quantitative trait loci (QTL), metabolic pathways, genetic diversity, genes, proteins, germplasm, literature, ontologies and a fully-structured markers and sequences database integrated with genome browsers and maps from various published studies (genetic, physical, bin, etc.). In addition, Gramene now hosts a variety of web services including a Distributed Annotation Server (DAS), BLAST and a public MySQL database. Twice a year, Gramene releases a major build of the database and makes interim releases to correct errors or to make important updates to software and/or data.
Nucleic Acids Research 11/2010; 39(Database issue):D1085-94. · 8.03 Impact Factor
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ABSTRACT: 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. CMap is freely available, can run on a variety of database engines and uses only free and open software components. AVAILABILITY: http://www.gmod.org/cmap
Bioinformatics 08/2009; 25(22):3040-2. · 5.47 Impact Factor
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Bioinformatics. 01/2009; 25:3040-3042.
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Junjian Ni,
Anuradha Pujar, Ken Youens-Clark,
Immanuel Yap,
Pankaj Jaiswal,
Isaak Tecle,
Chih-Wei Tung,
Liya Ren,
William Spooner,
Xuehong Wei,
Shuly Avraham,
Doreen Ware,
Lincoln Stein,
Susan McCouch
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ABSTRACT: Gramene is a comparative information resource for plants that integrates data across diverse data domains. In this article, we describe the development of a quantitative trait loci (QTL) database and illustrate how it can be used to facilitate both the forward and reverse genetics research. The QTL database contains the largest online collection of rice QTL data in the world. Using flanking markers as anchors, QTLs originally reported on individual genetic maps have been systematically aligned to the rice sequence where they can be searched as standard genomic features. Researchers can determine whether a QTL co-localizes with other QTLs detected in independent experiments and can combine data from multiple studies to improve the resolution of a QTL position. Candidate genes falling within a QTL interval can be identified and their relationship to particular phenotypes can be inferred based on functional annotations provided by ontology terms. Mutations identified in functional genomics populations and association mapping panels can be aligned with QTL regions to facilitate fine mapping and validation of gene-phenotype associations. By assembling and integrating diverse types of data and information across species and levels of biological complexity, the QTL database enhances the potential to understand and utilize QTL information in biological research.
Database The Journal of Biological Databases and Curation 01/2009; 2009:bap005. · 2.07 Impact Factor
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Chengzhi Liang,
Pankaj Jaiswal,
Claire Hebbard,
Shuly Avraham,
Edward S Buckler,
Terry Casstevens,
Bonnie Hurwitz,
Susan McCouch,
Junjian Ni,
Anuradha Pujar, [......],
Liya Ren,
William Spooner,
Isaak Tecle,
Jim Thomason,
Chih-wei Tung,
Xuehong Wei,
Immanuel Yap, Ken Youens-Clark,
Doreen Ware,
Lincoln Stein
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ABSTRACT: Gramene (www.gramene.org) is a curated resource for genetic, genomic and comparative genomics data for the major crop species, including rice, maize, wheat and many other plant (mainly grass) species. Gramene is an open-source project. All data and software are freely downloadable through the ftp site (ftp.gramene.org/pub/gramene) and available for use without restriction. Gramene's core data types include genome assembly and annotations, other DNA/mRNA sequences, genetic and physical maps/markers, genes, quantitative trait loci (QTLs), proteins, ontologies, literature and comparative mappings. Since our last NAR publication 2 years ago, we have updated these data types to include new datasets and new connections among them. Completely new features include rice pathways for functional annotation of rice genes; genetic diversity data from rice, maize and wheat to show genetic variations among different germplasms; large-scale genome comparisons among Oryza sativa and its wild relatives for evolutionary studies; and the creation of orthologous gene sets and phylogenetic trees among rice, Arabidopsis thaliana, maize, poplar and several animal species (for reference purpose). We have significantly improved the web interface in order to provide a more user-friendly browsing experience, including a dropdown navigation menu system, unified web page for markers, genes, QTLs and proteins, and enhanced quick search functions.
Nucleic Acids Research 02/2008; 36(Database issue):D947-53. · 8.03 Impact Factor
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Pankaj Jaiswal,
Junjian Ni,
Immanuel Yap,
Doreen Ware,
William Spooner, Ken Youens-Clark,
Liya Ren,
Chengzhi Liang,
Wei Zhao,
Kiran Ratnapu,
Benjamin Faga,
Payan Canaran,
Molly Fogleman,
Claire Hebbard,
Shuly Avraham,
Steven Schmidt,
Terry M Casstevens,
Edward S Buckler,
Lincoln Stein,
Susan McCouch
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ABSTRACT: Rice, maize, sorghum, wheat, barley and the other major crop grasses from the family Poaceae (Gramineae) are mankind's most important source of calories and contribute tens of billions of dollars annually to the world economy (FAO 1999, http://www.fao.org; USDA 1997, http://www.usda.gov). Continued improvement of Poaceae crops is necessary in order to continue to feed an ever-growing world population. However, of the major crop grasses, only rice (Oryza sativa), with a compact genome of approximately 400 Mbp, has been sequenced and annotated. The Gramene database (http://www.gramene.org) takes advantage of the known genetic colinearity (synteny) between rice and the major crop plant genomes to provide maize, sorghum, millet, wheat, oat and barley researchers with the benefits of an annotated genome years before their own species are sequenced. Gramene is a one stop portal for finding curated literature, genetic and genomic datasets related to maps, markers, genes, genomes and quantitative trait loci. The addition of several new tools to Gramene has greatly facilitated the potential for comparative analysis among the grasses and contributes to our understanding of the anatomy, development, environmental responses and the factors influencing agronomic performance of cereal crops. Since the last publication on Gramene database by D. H. Ware, P. Jaiswal, J. Ni, I. V. Yap, X. Pan, K. Y. Clark, L. Teytelman, S. C. Schmidt, W. Zhao, K. Chang et al. [(2002), Plant Physiol., 130, 1606-1613], the database has undergone extensive changes that are described in this publication.
Nucleic Acids Research 02/2006; 34(Database issue):D717-23. · 8.03 Impact Factor
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ABSTRACT: The Genetic Diversity module of the Gramene database ("http://www.gramene.org/diversity":http://www.gramene.org/diversity) is specifically designed to handle data from high-throughput sequencing and array-based genotyping plateforms. Empowered by the Genomic Diversity and Phenotype Data Model, Gramene Genetic Diversity module provides live database connectivities of RFLP, SSR and SNP allele data, information about QTL, passport data for wild and cultivated germplasm from rice, maize, wheat, and _Arabidopsis_, and quantitative phenotypic data for some of these accessions. Large datasets of SNP variation are searchable via genomic positions of interest by SNP Query tool on a sequenced genome; and, trait associations, patterns of linkage disequilibrium and diversity can be evaluated using TASSEL. The Gramene database is updated twice a year, with the most recent release (Build #31) completed in May 2010.
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