Phylo-VISTA: interactive visualization of multiple DNA sequence alignments
Phylo-VISTA: interactive visualization of multiple DNA sequence alignments
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DOI：
10.1093/bioinformatics/btg459
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发表时间：
2004-03-22
期刊：
影响因子：
5.8
通讯作者：
Dubchak, I
中科院分区：
文献类型：
--
作者：
Shah, N;Couronne, O;Dubchak, I
动机：多序列比较对生物学发现的作用已得到充分证实。随着越来越多的生物体产生了越来越多的基因组序列数据集，对可视化和比较跨物种比对数据的新能力的需求日益增强。为了提高效率，这些可视化算法必须支持在基于系统发育关系的比较框架中一致地适应大范围的进化距离的能力。结果：我们开发了Phylo-VISTA，这是一个交互式工具，通过可视化多个DNA序列的相似性测量来分析多个比对。视觉呈现的复杂性通过基于种间系统发育关系的框架有效地组织起来。系统发育组织支持快速、用户引导的物种间比较。为了帮助在大型序列数据集中导航，Phylo-VISTA利用了VISTA的概念，为用户提供了以不同分辨率选择和查看数据的能力。将多分辨率数据可视化与分析相结合，结合种间比较的系统发育框架，为多序列比对的可视化数据分析提供了高度灵活和强大的工具。
Motivation: The power of multi-sequence comparison for biological discovery is well established. The need for new capabilities to visualize and compare cross-species alignment data is intensified by the growing number of genomic sequence datasets being generated for an ever-increasing number of organisms. To be efficient these visualization algorithms must support the ability to accommodate consistently a wide range of evolutionary distances in a comparison framework based upon phylogenetic relationships.Results: We have developed Phylo-VISTA, an interactive tool for analyzing multiple alignments by visualizing a similarity measure for multiple DNA sequences. The complexity of visual presentation is effectively organized using a framework based upon interspecies phylogenetic relationships. The phylogenetic organization supports rapid, user-guided interspecies comparison. To aid in navigation through large sequence datasets, Phylo-VISTA leverages concepts from VISTA that provide a user with the ability to select and view data at varying resolutions. The combination of multiresolution data visualization and analysis, combined with the phylogenetic framework for interspecies comparison, produces a highly flexible and powerful tool for visual data analysis of multiple sequence alignments.