Reiser Leonore, Subramaniam Shabari, Zhang Peifen, Berardini Tanya
Phoenix Bioinformatics, Newark, California, USA.
Computercraft, Washington, District of Columbia, Columbia, USA.
Curr Protoc. 2022 Oct;2(10):e574. doi: 10.1002/cpz1.574.
The Arabidopsis Information Resource (TAIR; http://arabidopsis.org) is a comprehensive web resource of Arabidopsis biology for plant scientists. TAIR curates and integrates information about genes, proteins, gene function, orthologs, gene expression, mutant phenotypes, biological materials such as clones and seed stocks, genetic markers, genetic and physical maps, genome organization, images of mutant plants, protein sub-cellular localizations, publications, and the research community. The various data types are extensively interconnected and can be accessed through a variety of web-based search and display tools. This article primarily focuses on some basic methods for searching, browsing, visualizing, and analyzing information about Arabidopsis genes and genomes. Additionally, we describe how members of the community can share data via JBrowse and the Generic Online Annotation Submission Tool (GOAT) in order to make their published research more accessible and visible. © 2022 Wiley Periodicals LLC. Basic Protocol 1: TAIR homepage, sitemap, and navigation Basic Protocol 2: Finding comprehensive information about Arabidopsis genes Basic Protocol 3: Using the Arabidopsis genome browser: JBrowse Basic Protocol 4: Using the Gene Ontology annotations for gene discovery and gene function analysis Basic Protocol 5: Using gene lists to download bulk datasets Basic Protocol 6: Using TAIR's analysis tools to find short sequences and motifs Basic Protocol 7: Using the TAIR generic online annotation tool (GOAT) to submit functional annotations for Arabidopsis (or any other species) genes Basic Protocol 8: Using PhyloGenes to visualize gene families and predict functions Basic Protocol 9: Using TAIR to browse Arabidopsis literature Basic Protocol 10: Using the synteny viewer to find and display syntenic regions from Arabidopsis and other plant species.
拟南芥信息资源库（TAIR；http://arabidopsis.org）是一个面向植物科学家的拟南芥生物学综合网络资源库。TAIR整理并整合了有关基因、蛋白质、基因功能、直系同源基因、基因表达、突变体表型、生物材料（如克隆和种子库）、遗传标记、遗传图谱和物理图谱、基因组组织、突变体植物图像、蛋白质亚细胞定位、出版物以及研究群体等方面的信息。各种数据类型相互之间广泛关联，可通过多种基于网络的搜索和显示工具进行访问。本文主要聚焦于一些搜索、浏览、可视化和分析拟南芥基因及基因组信息的基本方法。此外，我们还描述了该群体的成员如何通过JBrowse和通用在线注释提交工具（GOAT）共享数据，以使他们已发表的研究更易于获取和更具可见性。© 2022威利期刊有限责任公司。基本方案1：TAIR主页、站点地图和导航 基本方案2：查找拟南芥基因的全面信息 基本方案3：使用拟南芥基因组浏览器：JBrowse 基本方案4：使用基因本体注释进行基因发现和基因功能分析 基本方案5：使用基因列表下载批量数据集 基本方案6：使用TAIR的分析工具查找短序列和基序 基本方案7：使用TAIR通用在线注释工具（GOAT）提交拟南芥（或任何其他物种）基因的功能注释 基本方案8：使用系统发育基因可视化基因家族并预测功能 基本方案9：使用TAIR浏览拟南芥文献 基本方案10：使用同线性查看器查找并显示拟南芥和其他植物物种的同线性区域。
