Center for Bioinformatics, National Laboratory of Protein Engineering and Plant Genetic Engineering, College of Life Sciences, Peking University, Beijing 100871, PR China.
BMC Genomics. 2011 Mar 30;12:165. doi: 10.1186/1471-2164-12-165.
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.
两个亚种（粳稻和籼稻）的水稻基因组序列同时发布，促进了水稻全基因组水平的研究。自高通量分析出现以来，大量的功能基因组数据迅速产生，使得集成的在线基因组浏览器成为科学家可视化和分析这些数据所不可或缺的工具。基于下一代网络技术和高通量实验数据，我们开发了 Rice-Map，这是一个新型的基因组浏览器，供研究人员交互式地浏览、分析和注释水稻基因组。
已经编译并加载到 Rice-Map 中的超过一百个注释轨道（81 个用于粳稻，82 个用于籼稻）。这些预先计算的注释涵盖了基因模型、转录证据、表达谱、表观遗传修饰、种间和种内同源性、遗传标记和其他基因组特征。除了这些预先计算的轨道外，注册用户还可以通过 Rice-Map 的 User-Defined Annotation 项交互式地添加注释和研究笔记。通过平滑滚动、拖动和缩放，用户可以在多个尺度上同时浏览各种基因组特征。通过专门的生物信息学分析平台（如 WebLab 和 Galaxy）可以对选定的条目进行即时分析。此外，还提供了一个基于 BioMart 的数据仓库“Rice Mart”，供高级用户根据复杂的标准获取批量数据集。
Rice-Map 提供了丰富的最新粳稻和籼稻注释，为计算和实验生物学家提供了有价值的资源。Rice-Map 可在 http://www.ricemap.org/ 上公开访问，所有数据均可免费下载。
