Shah Nameeta, Couronne Olivier, Pennacchio Len A, Brudno Michael, Batzoglou Serafim, Bethel E Wes, Rubin Edward M, Hamann Bernd, Dubchak Inna
Center for Image Processing and Integrated Computing, Department of Computer Science, One Shields Avenue, University of California, Davis, CA 95616-8562, USA.
Bioinformatics. 2004 Mar 22;20(5):636-43. doi: 10.1093/bioinformatics/btg459. Epub 2004 Jan 22.
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.
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.
Phylo-VISTA is available at http://www-gsd.lbl.gov/phylovista. It requires an Internet browser with Java Plug-in 1.4.2 and it is integrated into the global alignment program LAGAN at http://lagan.stanford.edu
多序列比对在生物学发现中的强大作用已得到充分证实。随着为越来越多的生物体生成的基因组序列数据集数量不断增加，对可视化和比较跨物种比对数据的新功能的需求也日益增强。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始终如一地适应广泛进化距离的能力。
我们开发了Phylo-VISTA，这是一个用于通过可视化多个DNA序列的相似性度量来分析多重比对的交互式工具。使用基于物种间系统发育关系的框架有效地组织了视觉呈现的复杂性。系统发育组织支持快速的、用户引导的物种间比较。为了帮助在大型序列数据集中进行导航，Phylo-VISTA利用了VISTA中的概念，为用户提供了在不同分辨率下选择和查看数据的能力。多分辨率数据可视化和分析的结合，以及用于物种间比较的系统发育框架，产生了一个用于多重序列比对视觉数据分析的高度灵活且强大的工具。
Phylo-VISTA可在http://www-gsd.lbl.gov/phylovista获得。它需要一个安装了Java插件1.4.2的互联网浏览器，并且已集成到http://lagan.stanford.edu的全局比对程序LAGAN中
