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GenExp:一个具有客户端数据呈现功能的交互式基于网络的基因组 DAS 客户端。

GenExp: an interactive web-based genomic DAS client with client-side data rendering.

机构信息

Software Department, UPC-BarcelonaTech, Barcelona, Spain.

出版信息

PLoS One. 2011;6(7):e21270. doi: 10.1371/journal.pone.0021270. Epub 2011 Jul 5.


DOI:10.1371/journal.pone.0021270
PMID:21750706
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC3130039/
Abstract

BACKGROUND: The Distributed Annotation System (DAS) offers a standard protocol for sharing and integrating annotations on biological sequences. There are more than 1000 DAS sources available and the number is steadily increasing. Clients are an essential part of the DAS system and integrate data from several independent sources in order to create a useful representation to the user. While web-based DAS clients exist, most of them do not have direct interaction capabilities such as dragging and zooming with the mouse. RESULTS: Here we present GenExp, a web based and fully interactive visual DAS client. GenExp is a genome oriented DAS client capable of creating informative representations of genomic data zooming out from base level to complete chromosomes. It proposes a novel approach to genomic data rendering and uses the latest HTML5 web technologies to create the data representation inside the client browser. Thanks to client-side rendering most position changes do not need a network request to the server and so responses to zooming and panning are almost immediate. In GenExp it is possible to explore the genome intuitively moving it with the mouse just like geographical map applications. Additionally, in GenExp it is possible to have more than one data viewer at the same time and to save the current state of the application to revisit it later on. CONCLUSIONS: GenExp is a new interactive web-based client for DAS and addresses some of the short-comings of the existing clients. It uses client-side data rendering techniques resulting in easier genome browsing and exploration. GenExp is open source under the GPL license and it is freely available at http://gralggen.lsi.upc.edu/recerca/genexp.

摘要

背景:分布式标注系统(DAS)提供了一种用于共享和整合生物序列标注的标准协议。目前有超过 1000 个 DAS 源,并且这个数字还在稳步增加。客户端是 DAS 系统的重要组成部分,它整合来自多个独立源的数据,以便为用户创建有用的表示。虽然有基于 Web 的 DAS 客户端,但它们大多数没有直接的交互功能,例如使用鼠标进行拖放和缩放。

结果:在这里,我们介绍了 GenExp,这是一个基于 Web 的、完全交互式的可视化 DAS 客户端。GenExp 是一个面向基因组的 DAS 客户端,能够从碱基级别到完整染色体的范围内创建基因组数据的有意义的表示。它提出了一种新颖的基因组数据渲染方法,并使用最新的 HTML5 网络技术在客户端浏览器中创建数据表示。由于客户端渲染,大多数位置更改不需要向服务器发出网络请求,因此缩放和平移的响应几乎是即时的。在 GenExp 中,可以直观地移动鼠标来探索基因组,就像地理地图应用程序一样。此外,在 GenExp 中,可以同时拥有多个数据查看器,并将应用程序的当前状态保存下来,以便稍后再次访问。

结论:GenExp 是一个新的交互式基于 Web 的 DAS 客户端,解决了现有客户端的一些不足之处。它使用客户端数据渲染技术,使基因组浏览和探索更加容易。GenExp 是基于 GPL 许可证的开源软件,可以在 http://gralggen.lsi.upc.edu/recerca/genexp 上免费获得。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/cb87/3130039/3b46884cf63f/pone.0021270.g002.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/cb87/3130039/408e4af907fa/pone.0021270.g001.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/cb87/3130039/3b46884cf63f/pone.0021270.g002.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/cb87/3130039/408e4af907fa/pone.0021270.g001.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/cb87/3130039/3b46884cf63f/pone.0021270.g002.jpg

相似文献

[1]
GenExp: an interactive web-based genomic DAS client with client-side data rendering.

PLoS One. 2011-7-5

[2]
DASher: a stand-alone protein sequence client for DAS, the Distributed Annotation System.

Bioinformatics. 2009-5-15

[3]
myKaryoView: a light-weight client for visualization of genomic data.

PLoS One. 2011-10-26

[4]
Dalliance: interactive genome viewing on the web.

Bioinformatics. 2011-1-19

[5]
JBrowse: a next-generation genome browser.

Genome Res. 2009-9

[6]
Integrating sequence and structural biology with DAS.

BMC Bioinformatics. 2007-9-12

[7]
Dasty2, an Ajax protein DAS client.

Bioinformatics. 2008-9-15

[8]
The distributed annotation system.

BMC Bioinformatics. 2001

[9]
The Integrated Genome Browser: free software for distribution and exploration of genome-scale datasets.

Bioinformatics. 2009-8-4

[10]
Statistical Viewer: a tool to upload and integrate linkage and association data as plots displayed within the Ensembl genome browser.

BMC Bioinformatics. 2005-4-12

引用本文的文献

[1]
Scribl: an HTML5 Canvas-based graphics library for visualizing genomic data over the web.

Bioinformatics. 2012-11-19

本文引用的文献

[1]
easyDAS: automatic creation of DAS servers.

BMC Bioinformatics. 2011-1-18

[2]
Integrative genomics viewer.

Nat Biotechnol. 2011-1

[3]
The Integrated Genome Browser: free software for distribution and exploration of genome-scale datasets.

Bioinformatics. 2009-8-4

[4]
DASher: a stand-alone protein sequence client for DAS, the Distributed Annotation System.

Bioinformatics. 2009-5-15

[5]
Jalview Version 2--a multiple sequence alignment editor and analysis workbench.

Bioinformatics. 2009-5-1

[6]
Ensembl 2009.

Nucleic Acids Res. 2009-1

[7]
The UCSC Genome Browser Database: update 2009.

Nucleic Acids Res. 2009-1

[8]
Dasty2, an Ajax protein DAS client.

Bioinformatics. 2008-9-15

[9]
Integrating biological data--the Distributed Annotation System.

BMC Bioinformatics. 2008-7-22

[10]
Integrating sequence and structural biology with DAS.

BMC Bioinformatics. 2007-9-12

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