Maintenance and Development of RepeatMasker

RepeatMasker的维护与开发

• 批准号: 7288796
• 负责人: Arian Fredericus Anthonius Smit
• 金额: $ 36.9万
• 依托单位: INSTITUTE FOR SYSTEMS BIOLOGY
• 依托单位国家: 美国
• 财政年份: 2003
• 资助国家: 美国
• 起止时间: 2003-08-15 至 2009-06-30
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/7288796
• 关键词: Age; Bioinformatics; Classification Scheme; Code; Computer software; Consensus; Consensus Sequence; DNA Transposable Elements; Data; Databases; Detection; Development; Evolution; Facility Construction Funding Category; Genetic Recombination; Genome; Genomics; Grant; Internet; Knowledge; Label; Length; Libraries; Link; Maintenance; Masks; Modeling; Names; Numbers; Organism; Output; Phase; Phylogenetic Analysis; Phylogeny; Process; Protein Databases; Proteins; R44 grant; Range; Resolution; Services; Shotgun Sequencing; Site; Small Business Funding Mechanisms; Small Business Innovation Research Grant; Source Code; Staging; Standards of Weights and Measures; Transcript; Translating; Work; base; computerized tools; design; genome sequencing; improved; mammalian genome; programs; rapid growth; tool

DESCRIPTION (provided by applicant): Most eukaryotic genomes include vast numbers of interspersed repeats (IRs), which are the remnants of mostly selfishly amplified transposable elements. Transposable elements have an exceptionally wide- ranging mutagenic effect on genomes, while recognition of IRs provide unparalleled information on genome evolution and is crucial in many aspects of bioinformatics. This grant would continue support for the maintenance and further development of RepeatMasker, a computational tool that has become the de facto standard for identification and characterization of IRs, and support the development of RepeatModeler, a program designed to derive RepeatMasker-grade databases of IR consensus sequences. The source code for these tools are freely available to the public. Development will emphasize the following: a) With the rapid growth of sequenced mammalian species, the building of mammalian repeat libraries has become our highest priority. The RepeatModeler program already excels in its consensus building ability and IR classification scheme, but is still in an early phase and many modules need to be developed. b) RepeatMasker development will initially be focused on the annotation modules. These need to be parallelized and made auditable in order to link annotations to the relevant database entries. We also present strategies to improve RepeatMasker"s detection of ancient, highly fragmented IRs and of IRs in draft genomes, and one that allows it to recognize genomic recombination sites within IRs. c) For many applications of RepeatMasker, including interspecies genome alignments and inference of species phylogenies, knowledge of the age and species distribution of IRs is crucial. We aim to automate and refine the process of "phylogenetic labeling" of consensus sequences in the library. d) We will further develop our website, by adding our transcript prediction program FEAST, increasing the number of pre-analyzed genomes, expanding our new protein based repeat masking services, and optionally presenting data in a graphical form.

描述（由申请人提供）：大多数真核基因组都包括大量散布的重复序列（IRS），这些重复序列是大多数自私放大的转座元素的残余物。转座元素对基因组具有异常广泛的诱变作用，而对IRS的识别则提供了有关基因组进化的无与伦比的信息，并且在生物信息学的许多方面至关重要。该赠款将继续支持ReponMasker的维护和进一步开发，ReponMasker是一种计算工具，已成为IRS识别和表征的事实上的标准，并支持ReponModeler的开发，该计划旨在得出IR共识序列的ReponMasker级数据库。这些工具的源代码可向公众免费使用。开发将强调以下内容：a）随着测序哺乳动物物种的快速增长，哺乳动物重复文库的建设已成为我们的最高优先级。 RepotModeler程序已经在其共识建筑能力和IR分类方案方面表现出色，但仍处于早期阶段，需要开发许多模块。 b）最初将重点放在注释模块上。这些需要并行化并进行审核，以将注释链接到相关数据库条目。我们还提出了改善重复效果的策略，以对基因组草案中的古代，高度分散的IRS和IRS的检测，并允许其识别IRS内的基因组重组站点。c）c）对于Reproker的许多应用，包括跨性别的基因组基因组对准和cr ands cristory of per and progential of per and progential of Irs and of irs and per and per and per and ph and per and per and。标记“图书馆中的共识序列。d）我们将通过添加成绩单预测计划盛宴，增加预先分析的基因组的数量，扩大我们新的基于蛋白质的重复掩盖服务，并选择以图形形式显示数据，从而进一步开发我们的网站。