Visualization of large influenza virus sequence datasets using adaptively aggregated trees with sampling-based subscale representation.
Visualization of large influenza virus sequence datasets using adaptively aggregated trees with sampling-based subscale representation.
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DOI：
10.1186/1471-2105-9-237
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发表时间：
2008-05-16
影响因子：
3
通讯作者：
Tatusova TA
中科院分区：
文献类型：
--
作者：
Zaslavsky L;Bao Y;Tatusova TA
随着流感基因组序列数据量的快速增长，研究人员在选择数据集和探索数据方面需要机器的帮助。需要增强的可视化工具以易于理解的形式在网络上表示探索性分析的结果，并方便信息检索。我们开发了一种方法，将大型系统发育树以聚合形式可视化，并具有子尺度细节的特殊表示。初始聚合树表示是用自动选择的分辨率级别构建的，以适应可用的屏幕空间，并根据序列相似性选择终端组。默认的聚合表示可以由用户交互地改进。终端组中的结构和数据可变性使用与组的文本注释具有相同垂直大小的小树来显示。这些子尺度表示是使用相应终端群的系统抽样计算的。包含终端组的聚合树可以使用结构化元数据（如季节分布、地理位置等）的聚合进行注释。这些算法在NCBI流感病毒资源中用JavaScript实现。
With the amount of influenza genome sequence data growing rapidly, researchers need machine assistance in selecting datasets and exploring the data. Enhanced visualization tools are required to represent results of the exploratory analysis on the web in an easy-to-comprehend form and to facilitate convenient information retrieval. We developed an approach to visualize large phylogenetic trees in an aggregated form with a special representation of subscale details. The initial aggregated tree representation is built with a level of resolution automatically selected to fit into the available screen space, with terminal groups selected based on sequence similarity. The default aggregated representation can be refined by users interactively. Structure and data variability within terminal groups are displayed using small trees that have the same vertical size as the text annotation of the group. These subscale representations are calculated using systematic sampling from the corresponding terminal group. The aggregated tree containing terminal groups can be annotated using aggregation of structured metadata, such as seasonal distribution, geographic locations, etc. The algorithms are implemented in JavaScript within the NCBI Influenza Virus Resource.
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影响因子：
64.8
作者：
Ghedin, E;Sengamalay, NA;Salzberg, SL
通讯作者：
Salzberg, SL
影响因子：
5.8
作者：
Rost, U;Bornberg-Bauer, E
通讯作者：
Bornberg-Bauer, E
影响因子：
3
作者：
Chevenet F;Brun C;Bañuls AL;Jacq B;Christen R
通讯作者：
Christen R
DOI：
10.1073/pnas.082110799
发表时间：
2002-04-30
影响因子：
11.1
作者：
Plotkin, JB;Dushoff, J;Levin, SA
通讯作者：
Levin, SA
影响因子：
5.5
作者：
Wolf, Yuri I.;Viboud, Cecile;Lipman, David J.
通讯作者：
Lipman, David J.