TreeWiz: interactive exploration of huge trees
TreeWiz: interactive exploration of huge trees
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DOI：
10.1093/bioinformatics/18.1.109
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发表时间：
2002-01-01
期刊：
影响因子：
5.8
通讯作者：
Bornberg-Bauer, E
中科院分区：
文献类型：
--
作者：
Rost, U;Bornberg-Bauer, E
动机：快速增长的数量和差异的生物数据需要解释在许多层次的描述。人的判断和直觉很重要，因为不是所有的数据都能自动和全面地分析。树和对应于某些特征的亚结构的可视化经常用于分析系统发育或分类。不幸的是，大多数现有的工具不能处理当前数据集的大小或所需的功能，或者两者兼而有之。结果：我们介绍了一个巨大树木的可视化程序，以及它们内容的交互式探索。我们已经制定了一系列针对生物学问题的新方案。用户可以从SWISS-PROT等标准数据库中获得概述、放大、过滤数据和检索细节。此外，还可以分析二级表示上由共同特征指定的所选叶集之间的关系。在PC（大约512 MB RAM）上，可以加载多达数万片叶子的树，并快速交互式地进行探索。我们演示了使用该程序对添加PFAM结构域作为特征的SYSTERS数据集（其中包含分层聚类的蛋白质序列）进行分析。
Motivation: The rapidly increasing amount and disparity of biological data requires interpretation at many levels of description. Human judgement and intuition are important because not all data can be automatically and comprehensively analyzed. Visualization of trees and substructures corresponding to certain features are often used to analyze phylogenies or taxonomies. Unfortunately, most existing tools do not cope with the size of current datasets, the required functionality, or both.Results: We introduce a program for visualization of huge trees and also for the interactive exploration of their content. We have developed a range of new schemes which are tailored for biological problems. Users can get an overview, zoom in, filter out data and retrieve details from standard databases such as SWISS-PROT. Furthermore, it is possible to analyze the relationship between chosen leaf sets that are specified by common features on a second level of representation. On a PC (with approximate to 512 MB RAM), trees of up to several tens of thousands of leaves can be loaded and both rapidly and interactively explored. We demonstrate the use of this program for the analysis of the SYSTERS data set (which contains hierarchically clustered protein sequences) to which PFAM domains were added as features.