Visualizing the genome: techniques for presenting human genome data and annotations
Visualizing the genome: techniques for presenting human genome data and annotations
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DOI：
10.1186/1471-2105-3-19
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发表时间：
2002-01-01
影响因子：
3
通讯作者：
Helt, GA
中科院分区：
文献类型：
--
作者：
Loraine, AE;Helt, GA
背景：为了充分利用新获取的公共人类基因组序列数据及相关注释，生物学家需要可视化工具（“基因组浏览器”），以适应人类基因中可变剪接的高频率及其他复杂性。
结果：在本文中，我们描述了以交互式图形格式呈现人类基因组序列数据和注释的可视化技术。这些技术包括：一维语义缩放，以在基因结构旁展示序列数据；对外显子进行颜色编码以指示翻译框架；可调节、可移动的层级，以便更轻松地查看基因组场景；以及在基因结构旁展示蛋白质注释，以显示可变剪接如何影响蛋白质结构和功能。这些技术通过两个基因组浏览器应用的实例进行了说明：Neomorphic GeneViewer注释工具和ProtAnnot（一个在基因组序列背景下展示蛋白质注释的原型浏览器）。
结论：通过介绍基因组数据可视化技术，我们希望为感兴趣的软件开发人员提供一份指南，说明在生物学家试图理解快速增长的公共基因组数据和注释时，哪些功能最有可能满足他们的需求。
Background: In order to take full advantage of the newly available public human genome sequence data and associated annotations, biologists require visualization tools ("genome browsers") that can accommodate the high frequency of alternative splicing in human genes and other complexities.Results: In this article, we describe visualization techniques for presenting human genomic sequence data and annotations in an interactive, graphical format. These techniques include: one-dimensional, semantic zooming to show sequence data alongside gene structures; color-coding exons to indicate frame of translation; adjustable, moveable tiers to permit easier inspection of a genomic scene; and display of protein annotations alongside gene structures to show how alternative splicing impacts protein structure and function. These techniques are illustrated using examples from two genome browser applications: the Neomorphic GeneViewer annotation tool and ProtAnnot, a prototype viewer which shows protein annotations in the context of genomic sequence.Conclusion: By presenting techniques for visualizing genomic data, we hope to provide interested software developers with a guide to what features are most likely to meet the needs of biologists as they seek to make sense of the rapidly expanding body of public genomic data and annotations.