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

基本信息

批准号：
10714226
负责人：
Robert MacDonald Hubley
金额：
$ 54.06万
依托单位：
INSTITUTE FOR SYSTEMS BIOLOGY
依托单位国家：
美国
项目类别：
财政年份：
2018
资助国家：
美国
起止时间：
2018-08-15 至 2028-06-30
项目状态：
未结题

来源：
https://reporter.nih.gov/project-details/10714226
关键词：
Biological databases Classification Collection Common Data Element Communities Complex Computer software Consensus Sequence DNA DNA Transposable Elements Data Data Commons Data Set Databases Detection Development Educational workshop Elements Evolution Excision Family Feedback Fostering Foundations Genome Grant Growth Human Genome Hybrids Knowledge Libraries Licensing Life Medical Metadata Methods Modeling Morphologic artifacts Mutation Polishes Proteins Publications Repetitive Sequence Research Research Institute Resources Scientist Sequence Alignment Sequence Analysis Source Training Work community engagement detection platform experience genetic information genome annotation genome-wide improved innovation interest markov model meetings method development mosaic novel pressure prototype reconstruction reference genome response success trustworthiness vertebrate genome

项目摘要

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. 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. During the life of this grant, the database has grown to include families belonging to more than 1000 species (from a baseline of 5). This growth has introduced a number of scale-based pressures, which in some cases have forced us to reduce Dfam functionality in response, and in other cases highlighted ways that the resource can better meet the needs of the community. Our proposed efforts largely target these matters while continuing to expand and diversify the resource.

项目概要/摘要重复DNA，尤其是由转座元件(TE) 引起的重复DNA，构成了许多基因组的很大一部分。对基因组中重复内容进行彻底、准确的注释取决于一个全面的数据库已知的 TE，以及用于识别元素腐烂实例的强大统计和程序方法并理清他们复杂的关系。 TE 实例的注释通常使用我们的 RepeatMasker 软件来执行，该软件会比较基因组到包含已知重复家族表示的数据库。这些都是历史上的共识序列，通常近似于原始 TE 的序列。我们的 Dfam 数据库是开放的访问重复DNA家族的集合，其中每个家族由多个序列表示对齐和轮廓隐马尔可夫模型（HMM）。我们已经证明了 Profile HMM 支持提高了注释敏感性，Dfam 为 TE 家族的管理者和那些使用生成的注释。在本次资助期间，数据库已发展到包含 1000 多个物种的科（从 5 的基线开始）。这种增长带来了许多基于规模的压力，在某些情况下迫使我们减少 Dfam 功能作为回应，并在其他情况下强调了资源的方式能够更好地满足社会的需求。我们提出的努力主要针对这些问题，同时继续扩大资源并使之多样化。