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PMID: 21450055 Published · epublish English Journal Article Research Support, Non-U.S. Gov't

Rice-Map: a new-generation rice genome browser.

BMC genomics ·Vol. 12 ·2011-03-30 ·Pages 165

Wang J, Kong L, Zhao S, Zhang H, Tang L, Li Z, Gu X, Luo J, Gao G

Abstract

The concurrent release of rice genome sequences for two subspecies (Oryza sativa L. ssp. japonica and Oryza sativa L. ssp. indica) facilitates rice studies at the whole genome level. Since the advent of high-throughput analysis, huge amounts of functional genomics data have been delivered rapidly, making an integrated online genome browser indispensable for scientists to visualize and analyze these data. Based on next-generation web technologies and high-throughput experimental data, we have developed Rice-Map, a novel genome browser for researchers to navigate, analyze and annotate rice genome interactively. More than one hundred annotation tracks (81 for japonica and 82 for indica) have been compiled and loaded into Rice-Map. These pre-computed annotations cover gene models, transcript evidences, expression profiling, epigenetic modifications, inter-species and intra-species homologies, genetic markers and other genomic features. In addition to these pre-computed tracks, registered users can interactively add comments and research notes to Rice-Map as User-Defined Annotation entries. By smoothly scrolling, dragging and zooming, users can browse various genomic features simultaneously at multiple scales. On-the-fly analysis for selected entries could be performed through dedicated bioinformatic analysis platforms such as WebLab and Galaxy. Furthermore, a BioMart-powered data warehouse "Rice Mart" is offered for advanced users to fetch bulk datasets based on complex criteria. Rice-Map delivers abundant up-to-date japonica and indica annotations, providing a valuable resource for both computational and bench biologists. Rice-Map is publicly accessible at http://www.ricemap.org/, with all data available for free downloading.

MeSH Terms
Chromosome Mapping DNA, Plant/genetics Epigenomics Expressed Sequence Tags Gene Expression Profiling Genes, Plant Genetic Markers Genome, Plant Internet Molecular Sequence Annotation Oryza/genetics Software User-Computer Interface
Chemicals
DNA, Plant Genetic Markers
Authors & Affiliations
9 authors, click to expand affiliations / ORCID
Wang Jun
Center for Bioinformatics, National Laboratory of Protein Engineering and Plant Genetic Engineering, College of Life Sciences, Peking University, Beijing 100871, PR China.
Kong Lei
Zhao Shuqi
Zhang He
Tang Liang
Li Zhe
Gu Xiaocheng
Luo Jingchu
Gao Ge
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Article Info
Journal
BMC genomics
Abbr.
BMC Genomics
ISSN
1471-2164
DOI
10.1186/1471-2164-12-165
Published
2011-03-30
Epub
2011-00-30
Pages
165
Language
English
Region
England
NLM ID
100965258
PMCID
PMC3072960
Subset
IM
External Links
PubMed source DOI: 10.1186/1471-2164-12-165 PMC Full Text View journal details
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