A framework for collaborative analysis of ENCODE data: Making large-scale analyses biologist-friendly
A framework for collaborative analysis of ENCODE data: Making large-scale analyses biologist-friendly
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DOI：
10.1101/gr.5578007
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发表时间：
2007-06-01
期刊：
影响因子：
7
通讯作者：
Nekrutenko, Anton
中科院分区：
文献类型：
--
作者：
Blankenberg, Daniel;Taylor, James;Nekrutenko, Anton
数据和工具的标准化和共享是大型合作项目（如DNA元素百科全书（ENCODE））的最大挑战。在这里，我们描述了一个紧凑的Web应用程序，银河2（ENCODE），有效地解决了这些问题。它为数据的存储和访问提供了一个直观的界面，并具有大量的分析工具，包括对基因组间隔的操作，用于操纵多个序列比对的实用程序和分子进化算法。通过提供数据和分析工具之间的直接联系，Galaxy2（ENCODE）允许解决现有软件无法解决的生物学问题。我们使用Galaxy2（ENCODE）来显示ENCODE区域在强纯化选择下包含>2000个可能具有功能的未注释的转录物。我们还表明，ENCODE区域是整个基因组的核苷酸取代率估计和比较它发表的数据的代表。虽然这些分析都很复杂，但从开始到结束都不超过15分钟。最后，我们将演示如何将新工具添加到Galaxy2（ENCODE）中。手稿的每一部分都补充了QuickTime的视频。Galaxy2（ENCODE）和屏幕录像可以在http://g2.bx.psu.edu上访问。
The standardization and sharing of data and tools are the biggest challenges of large collaborative projects such as the Encyclopedia of DNA Elements ( ENCODE). Here we describe a compact Web application, Galaxy2(ENCODE), that effectively addresses these issues. It provides an intuitive interface for the deposition and access of data, and features a vast number of analysis tools including operations on genomic intervals, utilities for manipulation of multiple sequence alignments, and molecular evolution algorithms. By providing a direct link between data and analysis tools, Galaxy2(ENCODE) allows addressing biological questions that are beyond the reach of existing software. We use Galaxy2(ENCODE) to show that the ENCODE regions contain >2000 unannotated transcripts under strong purifying selection that are likely functional. We also show that the ENCODE regions are representative of the entire genome by estimating the rate of nucleotide substitution and comparing it to published data. Although each of these analyses is complex, none takes more than 15 min from beginning to end. Finally, we demonstrate how new tools can be added to Galaxy2(ENCODE) with almost no effort. Every section of the manuscript is supplemented with QuickTime screencasts. Galaxy2(ENCODE) and the screencasts can be accessed at http://g2.bx.psu.edu.