Maintenance and Development of RepeatMasker and GESTALT

RepeatMasker和GESTALT的维护和开发

• 批准号: 6912723
• 负责人: Arian Fredericus Anthonius Smit
• 金额: $ 35.2万
• 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 2006-06-30
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/6912723
• 关键词: DNA replication; computer assisted sequence analysis; computer data analysis; computer graphics /printing; computer human interaction; computer program /software; computer system design /evaluation; gene duplication; genetic library; genome; interactive multimedia; molecular biology information system; systematic biology

DESCRIPTION (provided by applicant): The genomes of most eukaryotes 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 support maintenance and further development of RepeatMasker, a computational tool that has become the de facto standard for identification and characterization of IRs, and the GESTALT Workbench, a graphical user interface for detailed visualization of RepeatMasker results in their genomic context. The source codes of these tools are freely available to the academic community. Development will emphasize the following: a) RepeatMasker needs to be rewritten to allow expansion along with the increasing amount and variety of genomic sequence data. b) "Phylogenetic interpolation" will be used to construct repeat libraries for species for which only limited sequence is available (e.g. macaque, dog). This will be done by proper selection of the relevant subset of IR families from related species, and by applying appropriate, lineage-specific alignment parameters. c) Major expansion of the RepeatMasker functionalities of contamination detection and masking of only lineage specific IRs to facilitate the generation of interspecies genomic alignments. d) Building a public web server for RepeatMasker and GESTALT at the Institute for Systems Biology. This server will enable real-time analysis of private sequences, as well as offer pre-computed RepeatMasker results for all publicly available genomic sequences. It will also include novel repeat-based analysis services, such as genome sequence comparison, contamination detection and transcript prediction.

描述（由申请人提供）： 大多数真核生物的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；GESTALT Workbench 是一个图形用户界面，用于在基因组环境中详细可视化 RepeatMasker 结果。这些工具的源代码可以免费提供给学术界。发展将强调以下几点： a) RepeatMasker 需要重写，以允许随着基因组序列数据数量和种类的增加而扩展。 b) “系统发育插值”将用于为仅有有限序列可用的物种（例如猕猴、狗）构建重复文库。这将通过从相关物种中正确选择 IR 家族的相关子集并应用适当的谱系特异性比对参数来完成。 c) 主要扩展了 RepeatMasker 污染检测和仅屏蔽谱系特异性 IR 的功能，以促进种间基因组比对的生成。 d) 在系统生物学研究所为 RepeatMasker 和 GESTALT 构建公共 Web 服务器。该服务器将实现私有序列的实时分析，并为所有公开可用的基因组序列提供预先计算的 RepeatMasker 结果。它还将包括新颖的基于重复的分析服务，例如基因组序列比较、污染检测和转录本预测。