BBSRC-NSF/BIO Next generation collaborative annotation of genomes and synteny

基因组测序的物种数量正在迅速增加，随着英国（达尔文生命之树计划）和地球（地球生物基因组计划）正在进行的所有真核生物物种测序项目的开展，这种趋势将继续下去。为了使组装的基因组数据有意义，需要识别和描述蛋白质和非编码基因等重要特征；这个一般的过程称为注释。尽管自动标注基因组的方法取得了重大进展，但最准确的标注需要人工评估。然而，高昂的成本通常会阻碍对单个物种进行手动注释（带有精心策划的更新）。一种可扩展的替代方法是将手工工作直接用于参考数据集，并从更广泛的研究社区获取贡献。由此产生的高质量注释可以基于推断的同源性在物种之间进行投影。重要的是，用于注释的软件是快速、灵活和易于不同社区的注释者（专业管理员、实验室生物学家或好奇的非专家）使用的。在目前可用的基因组注释软件平台中，Artemis和Apollo是最受欢迎的两个，已经被广泛使用了20年。由桑格研究所开发的Artemis主要用于观察、注释和分析原核和真核微生物的基因组。阿尔忒弥斯的一个主要优势是其配套的“阿尔忒弥斯比较工具”（ACT），它允许在发现和探索基因组保护的背景下创建或编辑基因结构。Artemis和ACT的一个主要限制是，软件在大于几十兆的序列上表现不佳。像Artemis一样，Apollo最初是一个桌面工具，但后来被重新设计为一个基于web的工具，现在运行在共享服务器上，以便多个用户可以同时浏览和创建同一基因组的注释。Apollo可以轻松处理任何大小的基因组，并且可以很好地扩展多个并发用户。阿尔忒弥斯和阿波罗软件的开发已经并行进行了近20年。在某些情况下，伯克利的阿波罗团队和桑格的阿尔忒弥斯团队已经找到了查看和注释基因组数据的替代方法；但更多的时候，我们在目的和方法上找到了共同点。该应用程序将集成Artemis和Apollo的优点，以创建一个更高性能的注释平台。新的阿波罗将受益于现代和模块化的架构，协作开发和改进的可持续性。Apollo还将通过与EMBL-EBI小组合作开发的新数据接口进行增强，以便可以跨服务器访问基因组比较数据，并在探索协同性的上下文中执行注释。新一代的注释工具将取代现有的Artemis和Apollo项目，并集成到主要的基因组注释项目中，同时保留个人小规模用户的可用性。

The number of species with sequenced genomes is rising rapidly, and will continue to do so with projects to sequence all eukaryotic species in the UK (Darwin Tree of Life project) and on the planet (Earth Biogenome Project) underway. To make sense of assembled genome data important features, such as protein-and non-coding genes, need to be identified and described; this general process is called annotation. Despite major advances in methods to automatically annotate genomes, the most accurate annotations require human assessment. However, the prohibitive cost usually prevents manual annotation (with curated updates) from being performed on individual species. A scalable alternative is to direct manual effort towards reference datasets and to harvest contributions from the broader research community. The resulting high quality annotations can then be projected across species based on inferred homology. It is essential that the software used for annotation is fast, flexible and easy to use by different communities of annotators (professional curators, bench biologists, or curious non-experts). Of the currently available software platforms to annotate genomes, Artemis and Apollo are the two most popular and have been in wide use for 20 years. Artemis, developed at the Sanger Institute, has been used primarily for viewing, annotating and analysing the genomes of prokaryotic and eukaryotic microbes. A major strength of Artemis is its companion the 'Artemis Comparison Tool' (ACT) that allows gene structures to be created or edited in the context of discovering and exploring genome conservation. A major limitation of both Artemis and ACT is that the software performs badly on sequences larger than a few tens of megabases. Like Artemis, Apollo started as a desktop tool, but was redesigned as a web-based tool and now runs on a shared server so that multiple users can browse and create annotations across the same genome simultaneously. Apollo comfortably handles any size genome and scales well with multiple concurrent users.Development of Artemis and Apollo software has run in parallel for almost 20 years. The Berkeley-based Apollo team and the Sanger-based Artemis team have, in some cases, found alternative ways to view and annotate genome data; but more often, have found convergence in purpose and approach. The proposed application will integrate the best of Artemis and Apollo to create a single higher performance annotation platform. The new Apollo will benefit from modern and modular architecture, for collaborative development and improved sustainability. Apollo will also be enhanced with new data interfaces, developed in collaboration with the EMBL-EBI group, so that genome comparison data can be accessed across servers, and annotation performed in the context of exploring synteny.The new generation of annotation tool will replace the existing Artemis and Apollo projects and be integrated into major genome annotation projects as well as retaining is usability by individual small-scale users.