BambooGDB: a bamboo genome database with functional annotation and an analysis platform.
BambooGDB: a bamboo genome database with functional annotation and an analysis platform.
复制标题
BambooGDB：具有功能注释和分析平台的竹子基因组数据库
DOI：
10.1093/database/bau006
复制
发表时间：
2014
期刊：
影响因子：
--
通讯作者：
Jiang Z
中科院分区：
文献类型：
--
作者：
Zhao H;Peng Z;Fei B;Li L;Hu T;Gao Z;Jiang Z
竹子是世界上最重要的非木材林产品之一，也是生长最快的植物，是森林中唯一的主要草本植物。毛竹(Phyllostachys Edulis)首个高质量基因组草图序列的成功为研究毛竹的遗传和进化提供了新的视角。为了进一步扩大我们对竹子基因组的认识，在前人研究成果的基础上，我们开发了一个具有功能注释和分析平台的竹子基因组数据库BambooGDB。该数据库的主要内容是毛竹的从头测序数据，以及毛竹的全长互补DNA和RNA-SEQ数据。基于这些序列数据，对竹子基因组进行了全面的功能注释。此外，还构建了由比较基因组分析、蛋白质-蛋白质相互作用网络、路径分析和基因组数据可视化组成的分析平台。作为理解和识别竹子生物学机制的发现工具，该平台可以作为帮助和设计实验进行进一步验证的系统框架。此外，还纳入了各种强大的搜索工具和方便的浏览器，以方便这些数据的导航。据我们所知，这是第一个竹子基因组数据库。通过整合高通量测序数据、全功能注释和多个分析模块，BambooGDB旨在为全球研究人员提供中央基因组资源和可扩展的竹子基因组分析平台。BambooGDB可在http://www.bamboogdb.org/.上免费获得数据库地址：http://www.bamboogdb.org
Bamboo, as one of the most important non-timber forest products and fastest-growing plants in the world, represents the only major lineage of grasses that is native to forests. Recent success on the first high-quality draft genome sequence of moso bamboo (Phyllostachys edulis) provides new insights on bamboo genetics and evolution. To further extend our understanding on bamboo genome and facilitate future studies on the basis of previous achievements, here we have developed BambooGDB, a bamboo genome database with functional annotation and analysis platform. The de novo sequencing data, together with the full-length complementary DNA and RNA-seq data of moso bamboo composed the main contents of this database. Based on these sequence data, a comprehensively functional annotation for bamboo genome was made. Besides, an analytical platform composed of comparative genomic analysis, protein–protein interactions network, pathway analysis and visualization of genomic data was also constructed. As discovery tools to understand and identify biological mechanisms of bamboo, the platform can be used as a systematic framework for helping and designing experiments for further validation. Moreover, diverse and powerful search tools and a convenient browser were incorporated to facilitate the navigation of these data. As far as we know, this is the first genome database for bamboo. Through integrating high-throughput sequencing data, a full functional annotation and several analysis modules, BambooGDB aims to provide worldwide researchers with a central genomic resource and an extensible analysis platform for bamboo genome. BambooGDB is freely available at http://www.bamboogdb.org/. Database URL: http://www.bamboogdb.org
登录
查看更多内容
DOI：
10.1093/database/bas019
发表时间：
2012
期刊：
Database : the journal of biological databases and curation
影响因子：
--
作者：
Attwood TK;Coletta A;Muirhead G;Pavlopoulou A;Philippou PB;Popov I;Romá-Mateo C;Theodosiou A;Mitchell AL
通讯作者：
Mitchell AL
影响因子：
64.8
作者：
Matsumoto, T;Wu, JZ;Sugiura, M
通讯作者：
Sugiura, M
影响因子：
14.9
作者：
Harris, MA;Clark, J;White, R
通讯作者：
White, R
影响因子：
4.2
作者：
Das, M;Bhattacharya, S;Pal, A
通讯作者：
Pal, A
DOI：
10.2307/2412448
发表时间：
1970-01-01
期刊：
SYSTEMATIC ZOOLOGY
影响因子：
--
作者：
FITCH, WM
通讯作者：
FITCH, WM