Maintenance and Development of RepeatMasker

RepeatMasker的维护与开发

• 批准号: 7459675
• 负责人: Arian Fredericus Anthonius Smit
• 金额: $ 36.2万
• 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 2010-02-14
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/7459675
• 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）：大多数真核基因组包含大量散在重复序列（IR），它们是大多数自私扩增的转座元件的残余物。转座元件对基因组具有异常广泛的诱变作用，而IR的识别提供了关于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。这笔赠款将继续支持 RepeatMasker 的维护和进一步开发，RepeatMasker 是一种计算工具，已成为 IR 识别和表征的事实上的标准，并支持 RepeatModeler 的开发，RepeatModeler 是一个旨在派生 IR 共识的 RepeatMasker 级数据库的程序序列。这些工具的源代码可以免费向公众开放。开发将强调以下几点： 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构建已成为我们的首要任务。 RepeatModeler 程序在共识构建能力和 IR 分类方案方面已经表现出色，但仍处于早期阶段，许多模块需要开发。 b) RepeatMasker 开发最初将集中于注释模块。这些需要并行化并可审计，以便将注释链接到相关的数据库条目。我们还提出了改进 RepeatMasker 对古代、高度碎片化 IR 和草图基因组中 IR 的检测的策略，以及一种允许其识别 IR 内基因组重组位点的策略。 c) 对于 RepeatMasker 的许多应用，包括种间基因组比对和推理物种系统发育、IR 的年龄和物种分布的知识至关重要，我们的目标是自动化和完善文库中共有序列的“系统发育标记”过程。我们将进一步开发我们的网站，添加我们的转录预测程序 FEAST，增加预分析基因组的数量，扩展我们新的基于蛋白质的重复掩蔽服务，并可选择以图形形式呈现数据。