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

已测序基因组的物种数量正在迅速增加，并将继续这样做，正在进行的对英国(达尔文生命树计划)和地球上所有真核物种(地球生物基因组计划)进行排序的项目。为了理解组合的基因组数据，需要识别和描述重要的特征，如蛋白质和非编码基因；这一一般过程被称为注释。尽管在自动注释基因组的方法上取得了重大进展，但最准确的注释需要人工评估。然而，令人望而却步的成本通常会阻止对个别物种进行人工注释(经过精心策划的更新)。一种可扩展的替代方案是将人工工作引导到参考数据集，并从更广泛的研究社区获得贡献。由此产生的高质量注释可以基于推断的同源性跨物种进行投影。用于注释的软件必须是快速、灵活的，并且便于不同的注释者社区(专业的策展人、工作台生物学家或好奇的非专家)使用。在目前可用的基因组注释软件平台中，Artemis和Apollo是最受欢迎的两个平台，已经广泛使用了20年。由桑格研究所开发的Artemis主要用于查看、注释和分析原核和真核微生物的基因组。Artemis的一个主要优势是它的伙伴‘Artemis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，该软件在大于几十兆基数的序列上执行得很差。与Artemis一样，阿波罗最初是一个桌面工具，但被重新设计为基于网络的工具，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跨同一基因组的注释。阿波罗可以轻松地处理任何大小的基因组，并且可以很好地扩展到多个并发用户。Artemis和Apollo软件的开发已经并行运行了近20年。在某些情况下，伯克利的阿波罗团队和桑格的Artemis团队找到了查看和注释基因组数据的替代方法；但更多的情况下，他们在目的和方法上找到了共同点。拟议的应用程序将整合Artemis和Apollo的优点，以创建一个性能更高的单一注释平台。新的阿波罗将受益于现代化和模块化的架构，以实现协作开发和更好的可持续性。Apollo还将通过与EMBL-EBI小组合作开发的新数据接口得到增强，以便跨服务器访问基因组比较数据，并在探索共性的背景下进行注释。新一代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，并保留其可用性，供个别小规模用户使用。

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.