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.
| Original language | English (US) |
|---|---|
| Journal | Nucleic Acids Research |
| Volume | 36 |
| Issue number | SUPPL. 1 |
| DOIs | |
| State | Published - Jan 2008 |
| Externally published | Yes |
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ASJC Scopus subject areas
- Genetics
Cite this
Gramene : A growing plant comparative genomics resource. / Liang, Chengzhi; Jaiswal, Pankaj; Hebbard, Claire; Avraham, Shuly; Buckler, Edward S.; Casstevens, Terry; Hurwitz, Bonnie L; Mccouch, Susan; Ni, Junjian; Pujar, Anuradha; Ravenscroft, Dean; Ren, Liya; Spooner, William; Tecle, Isaak; Thomason, Jim; Tung, Chih Wei; Wei, Xuehong; Yap, Immanuel; Youens-Clark, Ken; Ware, Doreen; Stein, Lincoln.
In: Nucleic Acids Research, Vol. 36, No. SUPPL. 1, 01.2008.Research output: Contribution to journal › Article
}
TY - JOUR
T1 - Gramene
T2 - A growing plant comparative genomics resource
AU - Liang, Chengzhi
AU - Jaiswal, Pankaj
AU - Hebbard, Claire
AU - Avraham, Shuly
AU - Buckler, Edward S.
AU - Casstevens, Terry
AU - Hurwitz, Bonnie L
AU - Mccouch, Susan
AU - Ni, Junjian
AU - Pujar, Anuradha
AU - Ravenscroft, Dean
AU - Ren, Liya
AU - Spooner, William
AU - Tecle, Isaak
AU - Thomason, Jim
AU - Tung, Chih Wei
AU - Wei, Xuehong
AU - Yap, Immanuel
AU - Youens-Clark, Ken
AU - Ware, Doreen
AU - Stein, Lincoln
PY - 2008/1
Y1 - 2008/1
N2 - 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.
AB - 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.
UR - http://www.scopus.com/inward/record.url?scp=38549121882&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=38549121882&partnerID=8YFLogxK
U2 - 10.1093/nar/gkm968
DO - 10.1093/nar/gkm968
M3 - Article
C2 - 17984077
AN - SCOPUS:38549121882
VL - 36
JO - Nucleic Acids Research
JF - Nucleic Acids Research
SN - 0305-1048
IS - SUPPL. 1
ER -