SeqVISTA: a new module of integrated computational tools for studying transcriptional regulation
SeqVISTA: a new module of integrated computational tools for studying transcriptional regulation
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DOI：
10.1093/nar/gkh483
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发表时间：
2004-07-01
影响因子：
14.9
通讯作者：
Weng, ZP
中科院分区：
文献类型：
--
作者：
Hu, ZJ;Fu, YT;Weng, ZP
转录调控是细胞内最基本的调控机制之一。多种后生动物基因组序列的积累和高通量实验技术的出现推动了大量用于检测调控基序的生物信息学方法的发展。调控过程极其复杂，单个计算算法在基因组规模研究中的成功通常非常有限。在这里，我们论证了集成多个计算算法的重要性，并提出了一个集成了八个Web服务的基础设施，涵盖了转录调控的关键领域。我们采用了客户端集成技术，并使用一个通用的可视化工具SeqVISTA构建了一个一致的输入输出环境。该基础设施将允许轻松集成分散在互联网上的基因调控分析软件。它还将使工作台生物学家能够在熟悉的环境中使用尖端方法进行大量分析，生物信息学研究人员可以专注于开发新算法，而不需要在复杂的前或后处理器上投入大量精力。SeqVISTA对学术用户是免费的，只要安装了Java Web Start，就可以在http://zlab.bu.edu/SeqVISTA/web.jnlp，上在线启动。此外，该程序的独立版本可以下载并在本地运行。它可以在http://zlab.bu.edu/SeqVISTA.上获得
Transcriptional regulation is one of the most basic regulatory mechanisms in the cell. The accumulation of multiple metazoan genome sequences and the advent of high-throughput experimental techniques have motivated the development of a large number of bioinformatics methods for the detection of regulatory motifs. The regulatory process is extremely complex and individual computational algorithms typically have very limited success in genome-scale studies. Here, we argue the importance of integrating multiple computational algorithms and present an infrastructure that integrates eight web services covering key areas of transcriptional regulation. We have adopted the client-side integration technology and built a consistent input and output environment with a versatile visualization tool named SeqVISTA. The infrastructure will allow for easy integration of gene regulation analysis software that is scattered over the Internet. It will also enable bench biologists to perform an arsenal of analysis using cutting-edge methods in a familiar environment and bioinformatics researchers to focus on developing new algorithms without the need to invest substantial effort on complex pre- or post-processors. SeqVISTA is freely available to academic users and can be launched online at http://zlab.bu.edu/SeqVISTA/web.jnlp, provided that Java Web Start has been installed. In addition, a stand-alone version of the program can be downloaded and run locally. It can be obtained at http://zlab.bu.edu/SeqVISTA.