WormBase ParaSite - a comprehensive resource for helminth genomics.
WormBase ParaSite - a comprehensive resource for helminth genomics.
复制标题
DOI：
10.1016/j.molbiopara.2016.11.005
复制
发表时间：
2017-07
影响因子：
1.5
通讯作者：
Berriman M
中科院分区：
文献类型：
--
作者：
Howe KL;Bolt BJ;Shafie M;Kersey P;Berriman M
蠕虫库寄生虫是蠕虫基因组学研究的新资源。该资源提供了对100多种线虫和扁形蠕虫基因组的访问。基因组被一致地注解、组织和展示。提供了用于研究和查询数据的各种视图和工具。在过去的三年里，可公开获得的寄生虫基因组序列的数量急剧增加，对蠕虫功能基因组学的研究兴趣现在正在迅速加快，以回应这些集体努力奠定的基础。对于这些数据的组织、管理、分析和呈现，系统的方法显然对于最大化这些数据对研究人员的效用是至关重要的。我们开发了一个名为WormBase Parasite(http://parasite.wormbase.org))的门户网站，用于大规模询问蠕虫基因组。来自100多个线虫和扁形蠕虫物种的数据被整合，通过系统和一致的功能注释(例如蛋白质结构域和基因本体论术语)、基因表达分析(例如生命阶段特定转录组数据集的比对)和比较分析(例如直系同源和同源同源)来增加价值。我们提供了几种探索数据的方法，包括基因组浏览器、基因组和基因摘要页面、文本搜索、序列搜索、查询向导、批量下载和编程界面。在这篇综述中，我们概述了WormBase寄生虫背后的后端基础设施和分析，以及用户可用于询问蠕虫基因组数据的显示和工具。
WormBase ParaSite is a new resource for helminth genomics. The resource provides access to over 100 nematode and platyhelminth genomes. The genomes are consistently annotated, organised and presented. A variety of views and tools for exploring and querying the data are provided. The number of publicly available parasitic worm genome sequences has increased dramatically in the past three years, and research interest in helminth functional genomics is now quickly gathering pace in response to the foundation that has been laid by these collective efforts. A systematic approach to the organisation, curation, analysis and presentation of these data is clearly vital for maximising the utility of these data to researchers. We have developed a portal called WormBase ParaSite (http://parasite.wormbase.org) for interrogating helminth genomes on a large scale. Data from over 100 nematode and platyhelminth species are integrated, adding value by way of systematic and consistent functional annotation (e.g. protein domains and Gene Ontology terms), gene expression analysis (e.g. alignment of life-stage specific transcriptome data sets), and comparative analysis (e.g. orthologues and paralogues). We provide several ways of exploring the data, including genome browsers, genome and gene summary pages, text search, sequence search, a query wizard, bulk downloads, and programmatic interfaces. In this review, we provide an overview of the back-end infrastructure and analysis behind WormBase ParaSite, and the displays and tools available to users for interrogating helminth genomic data.