Analyzing HT-SELEX data with the Galaxy Project tools--A web based bioinformatics platform for biomedical research.
Analyzing HT-SELEX data with the Galaxy Project tools--A web based bioinformatics platform for biomedical research.
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DOI：
10.1016/j.ymeth.2015.10.008
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发表时间：
2016-03-15
期刊：
影响因子：
--
通讯作者：
Giangrande PH
中科院分区：
文献类型：
--
作者：
Thiel WH;Giangrande PH
用于研究以及诊断和治疗应用的DNA和RNA适配子的开发是一个快速增长的领域。在过去的十年中，随着高通量测序(HTS)的出现，识别适配子的过程发生了革命性的变化。然而，使普通分子生物学家能够分析这些大型数据集并加快识别候选适配子序列的生物信息学工具一直落后于HTS革命。银河计划是为了有效地分析基因组、外显子组和转录组HTS数据而开发的，我们现在已经将这些工具应用于适配HTS数据。Galaxy Project的公共Web服务器是一个开放源码的生物信息学工具集合，这些工具功能强大、灵活、动态且用户友好。Galaxy网络服务器的在线特性及其图形界面使用户无需编译代码或安装多个程序即可分析HTS数据。在此，我们介绍Galaxy网络服务器中的工具如何适用于对来自多轮选择的适体HTS数据进行预处理、编译、过滤和分析。
The development of DNA and RNA aptamers for research as well as diagnostic and therapeutic applications is a rapidly growing field. In the past decade, the process of identifying aptamers has been revolutionized with the advent of high-throughput sequencing (HTS). However, bioinformatics tools that enable the average molecular biologist to analyze these large datasets and expedite the identification of candidate aptamer sequences have been lagging behind the HTS revolution. The Galaxy Project was developed in order to efficiently analyze genome, exome, and transcriptome HTS data, and we have now applied these tools to aptamer HTS data. The Galaxy Project’s public webserver is an open source collection of bioinformatics tools that are powerful, flexible, dynamic, and user friendly. The online nature of the Galaxy webserver and its graphical interface allow users to analyze HTS data without compiling code or installing multiple programs. Herein we describe how tools within the Galaxy webserver can be adapted to pre-process, compile, filter and analyze aptamer HTS data from multiple rounds of selection.