Institute of Evolutionary Biology, University of Edinburgh, Edinburgh EH9 3JT, UK.
BMC Bioinformatics. 2013 Oct 7;14:301. doi: 10.1186/1471-2105-14-301.
Next-generation DNA sequencing technologies have made it possible to generate transcriptome data for novel organisms quickly and cheaply, to the extent that the effort required to annotate and publish a new transcriptome is greater than the effort required to sequence it. Often, following publication, details of the annotation effort are only available in summary form, hindering subsequent exploitation of the data. To promote best-practice in annotation and to ensure that data remain accessible, we have written afterParty, a web application that allows users to assemble, annotate and publish novel transcriptomes using only a web browser.
afterParty is a robust web application that implements best-practice transcriptome assembly, annotation, browsing, searching, and visualization. Users can turn a collection of reads (from Roche 454 chemistry) or assembled contigs (from any sequencing chemistry, including Illumina Solexa RNA-Seq) into a searchable, browsable transcriptome resource and quickly make it publicly available. Contigs are functionally annotated based on similarity to known sequences and protein domains. Once assembled and annotated, transcriptomes derived from multiple species or libraries can be compared and searched. afterParty datasets can either be created using the existing afterParty server, or using local instances that can be built easily using a virtual machine. afterParty includes powerful visualization tools for transcriptome dataset exploration and uses a flexible annotation architecture which will allow additional types of annotation to be added in the future.
afterParty's main use case scenario is one in which a working biologist has generated a large volume of transcribed sequence data and wishes to turn it into a useful resource that has some durability. By reducing the effort, bioinformatics skills, and computational resources needed to annotate and publish a transcriptome, afterParty will facilitate the annotation and sharing of sequence data that would otherwise remain unavailable. A typical metazoan transcriptome containing several tens of thousands of contigs can be annotated in a few minutes of interactive time and a few days of computational time.
下一代 DNA 测序技术使得快速、廉价地生成新生物体的转录组数据成为可能，以至于注释和发布新转录组所需的工作量大于测序所需的工作量。通常，在发表之后，注释工作的细节仅以摘要形式提供，这阻碍了数据的后续利用。为了促进注释的最佳实践并确保数据保持可访问性，我们编写了 afterParty，这是一个 Web 应用程序，仅使用 Web 浏览器即可允许用户组装、注释和发布新的转录组。
afterParty 是一个强大的 Web 应用程序，实现了最佳实践的转录组组装、注释、浏览、搜索和可视化。用户可以将一组读取（来自 Roche 454 化学）或组装的连续序列（来自任何测序化学，包括 Illumina Solexa RNA-Seq）转换为可搜索、可浏览的转录组资源，并快速将其公开。连续序列基于与已知序列和蛋白质结构域的相似性进行功能注释。组装和注释完成后，来自多个物种或文库的转录组可以进行比较和搜索。afterParty 数据集可以使用现有的 afterParty 服务器创建，也可以使用易于使用虚拟机构建的本地实例创建。afterParty 包括强大的转录组数据集探索可视化工具，并使用灵活的注释架构，该架构将允许在未来添加其他类型的注释。
afterParty 的主要用例场景是，当一位有实际工作经验的生物学家生成了大量转录序列数据并希望将其转化为具有一定耐久性的有用资源时。通过减少注释和发布转录组所需的工作量、生物信息学技能和计算资源，afterParty 将促进序列数据的注释和共享，否则这些数据将无法使用。一个包含数万个连续序列的典型后生动物转录组可以在几分钟的交互时间和几天的计算时间内完成注释。
