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: 10165778
• 负责人: Robert MacDonald Hubley
• 金额: $ 62.65万
• 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/10165778
• 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 Commons; Data Set; Data Sources; Data Storage and Retrieval; Databases; Development; Disincentive; Educational workshop; Elements; Evolution; FAIR principles; Family; Foundations; Funding; Generations; Genome; Growth; Human; Human Genome; 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; Visualization; Work; adjudication; annotation system; base; complex data; 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; sustainability framework; 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