Knowledge Management System of Kunming Institute of Botany,CAS
| 杜鹃花属基因组数据库的构建; Construction of a genome database for the genus Rhododendron | |
| 刘宁雅文 | |
| 导师 | 章成君 |
| 摘要 | The genus Rhododendron L. has been widely cultivated for hundreds of years around the world. Members of this genus are known for great ornamental and medicinal value. Owing to advances in sequencing technology, genomes and transcriptomes of members of the Rhododendron genus have been sequenced and published by various laboratories. With the increasing amounts of omics data, a centralized platform is necessary for effective storage, analysis, and integration of these large-scale datasets to ensure consistency, independence, and maintainability. Here, we report our development of the Rhododendron Plant Genome Database (RPGD; http://bioinfor.kib.ac.cn/RPGD/), which represents the first comprehensive database of Rhododendron genomics information. The platform is based on a LAMP (Linux + Apache + MariaDB + PHP) development environment and integrates data from multiple sources. RPGD provides a full visualization interface and various bioinformatics analysis modules. Firstly, RPGD contains raw data of R. delavayi which was produced by our team, and other raw data collected from public databases, including the genome sequences of R. williamsianum and R. simsii, raw data of RNA-Seq reads and full-length chloroplast genome sequences were presented as well. Secondly, these data have been extensively analyzed by bunch of software to provide the additional valuable information including functional annotation, gene expression profiles, gene families, transcription factor identification, homologous genes, and simple sequence repeats. In addition, a number of useful online tools were intergraded to RPGD to facilitate user processing and visualization of the retrieved data, including BLAST, JBrowse, Orthologous Groups, Genome Syntenic Browser, Flanking Sequence Finder, Expression Heatmap, Enrichment Analysis, and Batch Download. RPGD is designed to be a comprehensive and helpful platform for all Rhododendron researchers. Believe that RPGD will be an indispensable hub for Rhododendron studies. |
| 2021-05 | |
| 文献类型 | 学位论文 |
| 条目标识符 | http://ir.kib.ac.cn/handle/151853/74523 |
| 专题 | 昆明植物所硕博研究生毕业学位论文 |
| 推荐引用方式 GB/T 7714 | 刘宁雅文. 杜鹃花属基因组数据库的构建, Construction of a genome database for the genus Rhododendron[D],2021. |
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| 刘宁雅文-刘宁雅文硕士学位论文a3a33（7445KB） | 学位论文 | 限制开放 | CC BY-NC-SA | 请求全文 | ||
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