Poliakov Alexandre, Foong Justin, Brudno Michael, Dubchak Inna
US Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598, USA, Centre for Computational Medicine, Hospital for Sick Children, Toronto, ON M5G 1X8 Canada, Department of Computer Science, University of Toronto, Toronto, ON M5S 3G4 Canada and Genomics Division, LBNL, Berkeley, CA 94720, USA.
US Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598, USA, Centre for Computational Medicine, Hospital for Sick Children, Toronto, ON M5G 1X8 Canada, Department of Computer Science, University of Toronto, Toronto, ON M5S 3G4 Canada and Genomics Division, LBNL, Berkeley, CA 94720, USA US Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598, USA, Centre for Computational Medicine, Hospital for Sick Children, Toronto, ON M5G 1X8 Canada, Department of Computer Science, University of Toronto, Toronto, ON M5S 3G4 Canada and Genomics Division, LBNL, Berkeley, CA 94720, USA.
Bioinformatics. 2014 Sep 15;30(18):2654-5. doi: 10.1093/bioinformatics/btu355. Epub 2014 May 23.
With the ubiquitous generation of complete genome assemblies for a variety of species, efficient tools for whole-genome alignment along with user-friendly visualization are critically important. Our VISTA family of tools for comparative genomics, based on algorithms for pairwise and multiple alignments of genomic sequences and whole-genome assemblies, has become one of the standard techniques for comparative analysis. Most of the VISTA programs have been implemented as Web-accessible servers and are extensively used by the biomedical community. In this manuscript, we introduce GenomeVISTA: a novel implementation that incorporates most features of the VISTA family--fast and accurate alignment, visualization capabilities, GUI and analytical tools within a stand-alone software package. GenomeVISTA thus provides flexibility and security for users who need to conduct whole-genome comparisons on their own computers.
Implemented in Perl, C/C++ and Java, the source code is freely available for download at the VISTA Web site: http://genome.lbl.gov/vista/.
随着各种物种全基因组组装的普遍产生，用于全基因组比对的高效工具以及用户友好的可视化至关重要。我们基于基因组序列和全基因组组装的成对和多重比对算法的VISTA比较基因组学工具家族，已成为比较分析的标准技术之一。大多数VISTA程序已作为可通过网络访问的服务器实现，并被生物医学领域广泛使用。在本手稿中，我们介绍了GenomeVISTA：一种新颖的实现方式，它在一个独立软件包中整合了VISTA家族的大多数功能——快速准确的比对、可视化功能、图形用户界面和分析工具。因此，GenomeVISTA为需要在自己计算机上进行全基因组比较的用户提供了灵活性和安全性。
用Perl、C/C++和Java实现，源代码可在VISTA网站免费下载：http://genome.lbl.gov/vista/ 。
