Dfam: sustainable growth, curation support, and improved quality for mobile element annotation

项目摘要/摘要 重复DNA，特别是由转座元件(TES)引起的DNA，在许多基因组中占很大比例。 对基因组中重复内容的全面和准确的注释依赖于一个全面的数据库 已知的TES，以及用于识别元素的衰减实例的强大的统计和程序方法 并理清他们之间复杂的关系。 TE实例的注释通常使用我们的RepeatMasker软件执行，该软件可以比较基因组 添加到包含已知重复族的表示的数据库中。这些在历史上一直是共识 序列，其通常近似于原始TES的序列。最大的这类储藏库 Consensus Sequence是Repbase，其受限的许可证和有限的馆长界面导致缺乏 来自第三方的投入，以及创建许多独立的、往往是特定于生物体的开放数据库。平行线 这许多数据库的存在导致了命名和重复定义的分歧。 我们的DFAM数据库是一个开放访问的重复DNA家族集合，其中每个家族都有代表 通过多序列比对和轮廓隐马尔可夫模型(HMM)。我们已经证明了这一点 HMM支持改进的注释敏感度，DFAM为TE家族的两个策展人提供了许多帮助 以及那些使用所产生的注释的人。在这份提案中，我们描述了一项计划，以开发 DFAM的基础设施，以扩展到数千个基因组，并建立一个自给自足的TE数据公地 依赖于有限的集中管理。我们进一步描述了提高重复注记质量的计划 通过开发更可靠的比对判定方法，扩展可视化方法 这种复杂的数据类型，并改进TE子族的建模。 通过进一步开发这个开放获取数据库，我们将有力地遏制 独立的非标准重复数据集，减轻了开发TE的人员的数据管理负担 图书馆。

Project Summary / Abstract Repetitive DNA, especially that due to transposable elements (TEs), makes up a large fraction of many genomes. Thorough and accurate annotation of repetitive content in genomes depends on a comprehensive database of known TEs, along with robust statistical and procedural methods for recognizing decayed instances of elements and disentangling their complex relationships. Annotation of TE instances is usually performed using our RepeatMasker software, which compares a genome to a database containing representations of known repeat families. These have historically been consensus sequences, which generally approximate the sequences of the original TEs. The largest repository of such consensus sequences is Repbase, whose restrictive license and limited interface for curators has led to a lack of input from third parties and the creation of many unaffiliated, often organism-specific open databases. The parallel existence of these many databases has led to a divergence in nomenclature and repeat definition. Our Dfam database is an open access collection of repetitive DNA families, in which each family is represented by a multiple sequence alignment and a profile hidden Markov model (HMM). We have demonstrated that profile HMMs support improved annotation sensitivity, and Dfam provides numerous aids to both curators of TE families and those who make use of the resulting annotations. In this proposal, we describe a plan to develop the infrastructure of Dfam to expand to 1000s of genomes, and to establish a self-sustaining TE Data Commons dependent on limited centralized curation. We further describe plans to improve the quality of repeat annotation through development of methods for more reliable alignment adjudication, to expand approaches to visualization of this complex data type, and to improve the modeling of TE subfamilies. By further developing this open access database, we will provide a strong disincentive for the proliferation of unaffiliated non-standard repeat datasets and ease the burden of data management for those developing TE libraries.