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VISTA: computational tools for comparative genomics.VISTA：用于比较基因组学的计算工具
Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W273-9. doi: 10.1093/nar/gkh458.
2
VISTA family of computational tools for comparative analysis of DNA sequences and whole genomes.用于DNA序列和全基因组比较分析的VISTA计算工具家族。
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3
Multiple whole genome alignments and novel biomedical applications at the VISTA portal.VISTA门户网站上的多个全基因组比对及新型生物医学应用。
Nucleic Acids Res. 2007 Jul;35(Web Server issue):W669-74. doi: 10.1093/nar/gkm279. Epub 2007 May 8.
4
Dcode.org anthology of comparative genomic tools.Dcode.org比较基因组工具选集。
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5
Comparative analysis and visualization of genomic sequences using VISTA browser and associated computational tools.使用VISTA浏览器及相关计算工具对基因组序列进行比较分析和可视化。
Methods Mol Biol. 2007;395:3-16. doi: 10.1007/978-1-59745-514-5_1.
6
Obtaining comparative genomic data with the VISTA family of computational tools.使用VISTA系列计算工具获取比较基因组数据。
Curr Protoc Bioinformatics. 2009 Jun;Chapter 10:10.6.1-10.6.17. doi: 10.1002/0471250953.bi1006s26.
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ECR Browser: a tool for visualizing and accessing data from comparisons of multiple vertebrate genomes.ECR浏览器：一种用于可视化和访问来自多个脊椎动物基因组比较数据的工具。
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Multiple whole-genome alignments without a reference organism.无参考生物体的多个全基因组比对
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本文引用的文献

1
Aligning multiple genomic sequences with the threaded blockset aligner.使用线程化块集比对器对多个基因组序列进行比对。
Genome Res. 2004 Apr;14(4):708-15. doi: 10.1101/gr.1933104.
2
MAVID: constrained ancestral alignment of multiple sequences.MAVID：多条序列的受限祖先比对
Genome Res. 2004 Apr;14(4):693-9. doi: 10.1101/gr.1960404.
3
Automated whole-genome multiple alignment of rat, mouse, and human.大鼠、小鼠和人类全基因组自动多重比对。
Genome Res. 2004 Apr;14(4):685-92. doi: 10.1101/gr.2067704.
4
Characterization of evolutionary rates and constraints in three Mammalian genomes.三种哺乳动物基因组中进化速率和限制因素的特征分析。
Genome Res. 2004 Apr;14(4):539-48. doi: 10.1101/gr.2034704.
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Genome sequence of the Brown Norway rat yields insights into mammalian evolution.褐家鼠的基因组序列为哺乳动物进化研究提供了新见解。
Nature. 2004 Apr 1;428(6982):493-521. doi: 10.1038/nature02426.
6
Phylo-VISTA: interactive visualization of multiple DNA sequence alignments.系统发育可视化工具（Phylo-VISTA）：多个DNA序列比对的交互式可视化
Bioinformatics. 2004 Mar 22;20(5):636-43. doi: 10.1093/bioinformatics/btg459. Epub 2004 Jan 22.
7
Noncoding sequences conserved in a limited number of mammals in the SIM2 interval are frequently functional.在SIM2区间有限数量哺乳动物中保守的非编码序列通常具有功能。
Genome Res. 2004 Mar;14(3):367-72. doi: 10.1101/gr.1961204. Epub 2004 Feb 12.
8
Versatile and open software for comparing large genomes.用于比较大型基因组的通用且开放的软件。
Genome Biol. 2004;5(2):R12. doi: 10.1186/gb-2004-5-2-r12. Epub 2004 Jan 30.
9
Benchmarking tools for the alignment of functional noncoding DNA.用于功能性非编码DNA比对的基准测试工具。
BMC Bioinformatics. 2004 Jan 21;5:6. doi: 10.1186/1471-2105-5-6.
10
The dog genome: survey sequencing and comparative analysis.犬类基因组：测序与比较分析
Science. 2003 Sep 26;301(5641):1898-903. doi: 10.1126/science.1086432.

VISTA：用于比较基因组学的计算工具

VISTA: computational tools for comparative genomics.

作者信息

Frazer Kelly A, Pachter Lior, Poliakov Alexander, Rubin Edward M, Dubchak Inna

机构信息

Perlegen Sciences, Inc., 2021 Stierlin Court, Mountain View, CA 94043, USA.

出版信息

Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W273-9. doi: 10.1093/nar/gkh458.

DOI:10.1093/nar/gkh458
PMID:15215394
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC441596/
Abstract

Comparison of DNA sequences from different species is a fundamental method for identifying functional elements in genomes. Here, we describe the VISTA family of tools created to assist biologists in carrying out this task. Our first VISTA server at http://www-gsd.lbl.gov/vista/ was launched in the summer of 2000 and was designed to align long genomic sequences and visualize these alignments with associated functional annotations. Currently the VISTA site includes multiple comparative genomics tools and provides users with rich capabilities to browse pre-computed whole-genome alignments of large vertebrate genomes and other groups of organisms with VISTA Browser, to submit their own sequences of interest to several VISTA servers for various types of comparative analysis and to obtain detailed comparative analysis results for a set of cardiovascular genes. We illustrate capabilities of the VISTA site by the analysis of a 180 kb interval on human chromosome 5 that encodes for the kinesin family member 3A (KIF3A) protein.

摘要

比较不同物种的DNA序列是识别基因组中功能元件的基本方法。在此，我们描述了为协助生物学家完成这项任务而创建的VISTA工具家族。我们的第一个VISTA服务器（网址为http://www-gsd.lbl.gov/vista/ ）于2000年夏季推出，旨在比对长基因组序列，并将这些比对结果与相关功能注释进行可视化展示。目前，VISTA网站包含多个比较基因组学工具，为用户提供了丰富的功能，可通过VISTA浏览器浏览大型脊椎动物基因组和其他生物群体预先计算好的全基因组比对结果，将自己感兴趣的序列提交到多个VISTA服务器进行各种类型的比较分析，并获取一组心血管基因的详细比较分析结果。我们通过分析人类5号染色体上一个180 kb的区间（该区间编码驱动蛋白家族成员3A（KIF3A）蛋白）来说明VISTA网站的功能。