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Gramene: a growing plant comparative genomics resource Public Deposited

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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.
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  • Liang, C., Jaiswal, P., Hebbard, C., Avraham, S., Buckler, E. S., Casstevens, T., ... & Stein, L. (2008). Gramene: a growing plant comparative genomics resource. Nucleic Acids Research, 36, D947-D953. doi:10.1093/nar/gkm968
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  • 36
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  • The project is currently supported by National ScienceFoundation (0321685) and US Department of Agriculture-Agricultural Research Service specific cooperative agreement(58-1907-0-041). Funding to pay the OpenAccess publication charges for this article was provided byNational Science Foundation (0321685).
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  • description.provenance : Made available in DSpace on 2014-07-29T20:38:40Z (GMT). No. of bitstreams: 2 license_rdf: 1379 bytes, checksum: da3654ba11642cda39be2b66af335aae (MD5) JaiswalPankajBotanyPlantPathologyGrameneGrowingPlant.pdf: 5457936 bytes, checksum: 6d1df6cb242cbbd95a1eb097962ada08 (MD5) Previous issue date: 2007-11-04
  • description.provenance : Submitted by Erin Clark (erin.clark@oregonstate.edu) on 2014-07-29T20:38:27Z No. of bitstreams: 2 license_rdf: 1379 bytes, checksum: da3654ba11642cda39be2b66af335aae (MD5) JaiswalPankajBotanyPlantPathologyGrameneGrowingPlant.pdf: 5457936 bytes, checksum: 6d1df6cb242cbbd95a1eb097962ada08 (MD5)
  • description.provenance : Approved for entry into archive by Erin Clark(erin.clark@oregonstate.edu) on 2014-07-29T20:38:40Z (GMT) No. of bitstreams: 2 license_rdf: 1379 bytes, checksum: da3654ba11642cda39be2b66af335aae (MD5) JaiswalPankajBotanyPlantPathologyGrameneGrowingPlant.pdf: 5457936 bytes, checksum: 6d1df6cb242cbbd95a1eb097962ada08 (MD5)

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