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:10165778
- 负责人:
- 金额:$ 62.65万
- 依托单位:
- 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 2023-05-31
- 项目状态:已结题
- 来源:
- 关键词:Animal ModelArchitectureAwarenessBiological databasesCollaborationsCollectionCommon Data ElementCommunitiesComplexComputer softwareComputing MethodologiesConsensusConsensus SequenceDNADNA Transposable ElementsDataData CommonsData SetData SourcesData Storage and RetrievalDatabasesDevelopmentDisincentiveEducational workshopElementsEvolutionFAIR principlesFamilyFoundationsFundingGenerationsGenomeGrowthHumanHuman GenomeInfrastructureKnowledgeLibrariesLicensingMedicalMetadataMethodsModelingMovementMutationNomenclatureOrganismPaperProductionProtocols documentationPublicationsQuality ControlRepetitive SequenceResearchResearch InstituteResearch PersonnelResourcesSequence AlignmentSequence AnalysisSourceStandardizationSystemTaxonomyTimeTrainingTrustUnited States National Institutes of HealthUpdateVisualizationWorkadjudicationannotation systembasecomplex datadata managementdata modelingexpectationexperiencegenetic informationgenome annotationgenome browsergenome-wideimprovedinnovationmarkov modelmeetingsmethod developmentnoveloutreachreference genomerepositorysustainability frameworkvertebrate genomewhole 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. 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
项目成果
期刊论文数量(0)
专著数量(0)
科研奖励数量(0)
会议论文数量(0)
专利数量(0)
数据更新时间:{{ journalArticles.updateTime }}
{{
item.title }}
{{ item.translation_title }}
- DOI:
{{ item.doi }} - 发表时间:
{{ item.publish_year }} - 期刊:
- 影响因子:{{ item.factor }}
- 作者:
{{ item.authors }} - 通讯作者:
{{ item.author }}
数据更新时间:{{ journalArticles.updateTime }}
{{ item.title }}
- 作者:
{{ item.author }}
数据更新时间:{{ monograph.updateTime }}
{{ item.title }}
- 作者:
{{ item.author }}
数据更新时间:{{ sciAawards.updateTime }}
{{ item.title }}
- 作者:
{{ item.author }}
数据更新时间:{{ conferencePapers.updateTime }}
{{ item.title }}
- 作者:
{{ item.author }}
数据更新时间:{{ patent.updateTime }}
Robert MacDonald Hubley其他文献
Robert MacDonald Hubley的其他文献
{{
item.title }}
{{ item.translation_title }}
- DOI:
{{ item.doi }} - 发表时间:
{{ item.publish_year }} - 期刊:
- 影响因子:{{ item.factor }}
- 作者:
{{ item.authors }} - 通讯作者:
{{ item.author }}
{{ truncateString('Robert MacDonald Hubley', 18)}}的其他基金
Development and Maintenance of RepeatMasker and RepeatModeler
RepeatMasker和RepeatModeler的开发和维护
- 批准号:
10367846 - 财政年份:2022
- 资助金额:
$ 62.65万 - 项目类别:
Development and Maintenance of RepeatMasker and RepeatModeler
RepeatMasker和RepeatModeler的开发和维护
- 批准号:
10563214 - 财政年份:2022
- 资助金额:
$ 62.65万 - 项目类别:
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:
10714226 - 财政年份:2018
- 资助金额:
$ 62.65万 - 项目类别:
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 - 财政年份:2018
- 资助金额:
$ 62.65万 - 项目类别:
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:
10407543 - 财政年份:2018
- 资助金额:
$ 62.65万 - 项目类别:
相似海外基金
CAREER: Efficient Algorithms for Modern Computer Architecture
职业:现代计算机架构的高效算法
- 批准号:
2339310 - 财政年份:2024
- 资助金额:
$ 62.65万 - 项目类别:
Continuing Grant
Hardware-aware Network Architecture Search under ML Training workloads
ML 训练工作负载下的硬件感知网络架构搜索
- 批准号:
2904511 - 财政年份:2024
- 资助金额:
$ 62.65万 - 项目类别:
Studentship
CAREER: Creating Tough, Sustainable Materials Using Fracture Size-Effects and Architecture
职业:利用断裂尺寸效应和架构创造坚韧、可持续的材料
- 批准号:
2339197 - 财政年份:2024
- 资助金额:
$ 62.65万 - 项目类别:
Standard Grant
Travel: Student Travel Support for the 51st International Symposium on Computer Architecture (ISCA)
旅行:第 51 届计算机体系结构国际研讨会 (ISCA) 的学生旅行支持
- 批准号:
2409279 - 财政年份:2024
- 资助金额:
$ 62.65万 - 项目类别:
Standard Grant
Understanding Architecture Hierarchy of Polymer Networks to Control Mechanical Responses
了解聚合物网络的架构层次结构以控制机械响应
- 批准号:
2419386 - 财政年份:2024
- 资助金额:
$ 62.65万 - 项目类别:
Standard Grant
I-Corps: Highly Scalable Differential Power Processing Architecture
I-Corps:高度可扩展的差分电源处理架构
- 批准号:
2348571 - 财政年份:2024
- 资助金额:
$ 62.65万 - 项目类别:
Standard Grant
Collaborative Research: Merging Human Creativity with Computational Intelligence for the Design of Next Generation Responsive Architecture
协作研究:将人类创造力与计算智能相结合,设计下一代响应式架构
- 批准号:
2329759 - 财政年份:2024
- 资助金额:
$ 62.65万 - 项目类别:
Standard Grant
The architecture and evolution of host control in a microbial symbiosis
微生物共生中宿主控制的结构和进化
- 批准号:
BB/X014657/1 - 财政年份:2024
- 资助金额:
$ 62.65万 - 项目类别:
Research Grant
RACCTURK: Rock-cut Architecture and Christian Communities in Turkey, from Antiquity to 1923
RACCTURK:土耳其的岩石建筑和基督教社区,从古代到 1923 年
- 批准号:
EP/Y028120/1 - 财政年份:2024
- 资助金额:
$ 62.65万 - 项目类别:
Fellowship
NSF Convergence Accelerator Track M: Bio-Inspired Surface Design for High Performance Mechanical Tracking Solar Collection Skins in Architecture
NSF Convergence Accelerator Track M:建筑中高性能机械跟踪太阳能收集表皮的仿生表面设计
- 批准号:
2344424 - 财政年份:2024
- 资助金额:
$ 62.65万 - 项目类别:
Standard Grant