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

Dfam：可持续增长、管理支持和移动元素注释质量的提高

• 批准号: 9764454
• 负责人: Robert MacDonald Hubley
• 金额: $ 60.34万
• 依托单位: INSTITUTE FOR SYSTEMS BIOLOGY
• 依托单位国家: 美国
• 财政年份: 2018
• 资助国家: 美国
• 起止时间: 2018-08-15 至 2023-05-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/9764454
• 关键词: Animal Model; Architecture; Awareness; Biological databases; Collaborations; Collection; Common Data Element; Communities; Complex; Computer software; Computing Methodologies; Consensus; Consensus Sequence; DNA; DNA Transposable Elements; Data; Data Set; Data Sources; Data Storage and Retrieval; Databases; Development; Disincentive; Educational workshop; Elements; Evolution; Family; Foundations; Funding; Generations; Genome; Growth; Human; Human Genome; Imagery; Infrastructure; Knowledge; Libraries; Licensing; Medical; Metadata; Methods; Modeling; Movement; Mutation; Nomenclature; Organism; Paper; Production; Protocols documentation; Publications; Quality Control; Repetitive Sequence; Research; Research Institute; Research Personnel; Resources; Sequence Alignment; Sequence Analysis; Source; Standardization; System; Taxonomy; Time; Training; Trust; United States National Institutes of Health; Update; Work; adjudication; annotation system; base; data management; data modeling; expectation; experience; genetic information; genome annotation; genome browser; genome-wide; improved; innovation; markov model; meetings; method development; novel; outreach; reference genome; repository; vertebrate genome; whole genome

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.

项目摘要 /摘要 重复的DNA，特别是由于转座元素（TES），占许多基因组的很大一部分。 基因组中重复含量的彻底准确注释取决于一个综合数据库 已知的TE，以及可靠的统计和程序方法，用于识别元素的衰减实例 并解开他们复杂的关系。 通常使用我们的repotmasker软件进行TE实例的注释，该软件比较基因组 到包含已知重复系列表示的数据库。这些历史上已经达成共识 序列，通常近似原始TE的序列。最大的存储库 共识序列是repbase，其限制性许可和策展人的界面有限导致缺乏 来自第三方的输入以及创建许多非相关的，通常特定于有机体的开放数据库。平行 这些许多数据库的存在导致命名法和重复定义的差异。 我们的DFAM数据库是重复的DNA家族的开放访问集合，每个家族的代表 通过多个序列比对和配置文件隐藏的马尔可夫模型（HMM）。我们已经证明了该配置文件 HMMS支持提高注释敏感性，DFAM为TE家族的两个策展人提供了许多辅助工具 以及那些利用由此产生的注释的人。在此提案中，我们描述了制定的计划 DFAM的基础架构将扩展到1000秒的基因组，并建立自我维持的TE数据共享 取决于有限的集中策划。我们进一步描述了提高重复注释质量的计划 通过开发方法以进行更可靠的一致性裁决，扩展可视化方法 在这种复杂的数据类型中，并改善TE亚家族的建模。 通过进一步开发此开放访问数据库，我们将为扩散的强烈抑制 非相关的非标准重复数据集并减轻开发TE的人的数据管理负担 库。