Karolchik Donna, Hinrichs Angie S, Kent W James
Center for Biomolecular Science and Engineering, University of California Santa Cruz, Santa Cruz, California, USA.
Curr Protoc Bioinformatics. 2009 Dec;Chapter 1:Unit1.4. doi: 10.1002/0471250953.bi0104s28.
The University of California Santa Cruz (UCSC) Genome Browser is a popular Web-based tool for quickly displaying a requested portion of a genome at any scale, accompanied by a series of aligned annotation "tracks." The annotations-generated by the UCSC Genome Bioinformatics Group and external collaborators-display gene predictions, mRNA and expressed sequence tag alignments, simple nucleotide polymorphisms, expression and regulatory data, phenotype and variation data, and pairwise and multiple-species comparative genomics data. All information relevant to a region is presented in one window, facilitating biological analysis and interpretation. The database tables underlying the Genome Browser tracks can be viewed, downloaded, and manipulated using another Web-based application, the UCSC Table Browser. Users can upload data as custom annotation tracks in both browsers for research or educational use. This unit describes how to use the Genome Browser and Table Browser for genome analysis, download the underlying database tables, and create and display custom annotation tracks.
加利福尼亚大学圣克鲁兹分校（UCSC）基因组浏览器是一个广受欢迎的基于网络的工具，可快速显示基因组中任意规模的所需部分，并伴有一系列比对的注释“轨道”。这些注释由UCSC基因组生物信息学小组和外部合作者生成，显示基因预测、mRNA和表达序列标签比对、单核苷酸多态性、表达和调控数据、表型和变异数据以及成对和多物种比较基因组学数据。与一个区域相关的所有信息都在一个窗口中呈现，便于进行生物学分析和解读。基因组浏览器轨道所基于的数据库表可以使用另一个基于网络的应用程序UCSC表浏览器进行查看、下载和操作。用户可以在这两个浏览器中上传数据作为自定义注释轨道，用于研究或教育目的。本单元介绍如何使用基因组浏览器和表浏览器进行基因组分析、下载基础数据库表以及创建和显示自定义注释轨道。
