Database (Oxford). 2022 Feb 2;2022. doi: 10.1093/database/baab088.
Gene families contain genes that come from the same ancestor and have similar sequences and structures. They perform certain specific functions within and among different species. Currently, there is no complete process or platform for the rapid analysis of plant gene families. In this study, a comprehensive query and analysis platform of plant gene families, the Plant Gene Family Platform (PlantGF), was constructed. The platform is composed of four main parts: Search, Tools, Statistics and Auxiliary. A total of 2 909 580 gene family members were identified from 138 plant species in PlantGF. The data can be queried in the Search section through a user-friendly interface. A general process for gene family analysis, having nine steps, is provided. The platform also includes four online tools (HMM-Search, BLAST, MAFFT and HMMER) in the Tools section for useful additional analyses. The statistical analysis of the relevant gene families is shown on the Statistics page. Auxiliary pages are provided for data downloading. The datasets for all 138 plant species' protein sequences and their gene families can be acquired on the Download page. A user's manual and some useful links are displayed on the Manual and Links pages, respectively. To the best of our knowledge, PlantGF is the first comprehensive platform for studying plant gene families, and it will make important contributions to plant gene family-related research. Database URL: http://biodb.sdau.edu.cn/PGF/index.html.
基因家族包含来自同一祖先、具有相似序列和结构的基因。它们在不同物种的内部和之间执行某些特定功能。目前，还没有用于快速分析植物基因家族的完整过程或平台。在这项研究中，构建了一个植物基因家族的综合查询和分析平台，即植物基因家族平台（PlantGF）。该平台由四个主要部分组成：搜索、工具、统计和辅助。在 PlantGF 中，从 138 种植物中鉴定出了 2909580 个基因家族成员。这些数据可以通过用户友好的界面在搜索部分进行查询。该平台提供了一个通用的基因家族分析流程，共包含九个步骤。该平台还在工具部分包括四个在线工具（HMM-Search、BLAST、MAFFT 和 HMMER），用于进行有用的附加分析。在统计页面上显示了相关基因家族的统计分析。辅助页面提供了数据下载。在下载页面上，可以获取所有 138 种植物物种的蛋白质序列及其基因家族的数据集。用户手册和一些有用的链接分别显示在手册和链接页面上。据我们所知，PlantGF 是第一个用于研究植物基因家族的综合平台，它将为植物基因家族相关研究做出重要贡献。数据库网址：http://biodb.sdau.edu.cn/PGF/index.html。
