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Nucleic Acids Research Advance Access published online on November 4, 2007
Nucleic Acids Research, doi:10.1093/nar/gkm968
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© 2007 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Database Issue

Gramene: a growing plant comparative genomics resource

Chengzhi Liang1, Pankaj Jaiswal2, Claire Hebbard2, Shuly Avraham1, Edward S. Buckler3,4, Terry Casstevens3, Bonnie Hurwitz1, Susan McCouch2, Junjian Ni2, Anuradha Pujar2, Dean Ravenscroft2, Liya Ren1, William Spooner1, Isaak Tecle2, Jim Thomason1, Chih-wei Tung2, Xuehong Wei1, Immanuel Yap2, Ken Youens-Clark1, Doreen Ware1,4 and Lincoln Stein1,*

1Cold Spring Harbor Laboratory, 1 Bungtown Rd, Cold Spring Harbor, NY 11724, 2Department of Plant Breeding and Genetics, 240 Emerson Hall, 3Institute for Genomic Diversity and 4USDA-ARS NAA Plant, Soil & Nutrition Laboratory Research Unit, Cornell University, Ithaca, NY 14853, USA

*To whom correspondence should be addressed. Tel: 516 367 8380; Fax: 516 367 8389; Email: lstein{at}cshl.edu

Received September 20, 2007. Revised October 16, 2007. Accepted October 17, 2007.

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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