The ProPhylER Database and Web Resource

ProPhylER 数据库和网络资源

• 批准号: 7117404
• 负责人: AREND SIDOW
• 金额: $ 62.63万
• 依托单位: STANFORD UNIVERSITY
• 依托单位国家: 美国
• 财政年份: 2004
• 资助国家: 美国
• 起止时间: 2004-09-15 至 2008-08-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/7117404
• 关键词: Internet; evolution; genome; molecular biology information system; protein sequence; protein structure function; single nucleotide polymorphism

DESCRIPTION (provided by applicant): We propose to establish the ProPhylER (Protein Phylogeny and Evolutionary Rates) database as a web resource available to the general research community. The ProPhylER database will feature quantitative estimates of local constraint on orthologs and closely related paralogs. Estimates of constraint require robust, curated, alignments and phylogenetic trees, which ProPhylER generates as part of its dataflow. Alignments, trees, and estimates of constraint will be made available via graphical interfaces on the web site that will be developed. In addition, because ProPhylER's trees provide the natural framework for relating protein-coding genes and their annotation across model organism and genome databases, reciprocal links to SGD, Flybase, and the UCSC browser are proposed. We anticipate that ProPhylER will become a widely used tool for the analysis of functional constraint and phylogenetic relationships among related genes. Because ProPhylER's data are generated semiautomatically with curation at the critical steps in the dataflow, ProPhylER's data have a high degree of reliability that would be difficult to reproduce for individual investigators working on a particular protein. Thus, initially it will mostly be useful for experimentalists for whom analyses of constraint can guide structure function analyses, and for whom the curated alignments and phylogenetic trees will provide a knowledge base for the protein of interest. Extension of ProPhylER to generate quantitative predictions of the deleteriousness of cSNPs will expand the target community to include human geneticists and genomicists. As sequence data become less limiting for the majority of eukaryotic proteins, ProPhylER will expand to cover most of eukaryotic ortholog space and become the database that ties together eukaryotic orthologs and closely related paralogs by their evolutionary relationships.

描述（由申请人提供）： 我们建议建立 ProPhylER（蛋白质系统发育和进化速率）数据库作为一般研究界可用的网络资源。 ProPhylER 数据库将以直向同源物和密切相关的旁系同源物的局部约束的定量估计为特征。约束的估计需要强大的、精心策划的比对和系统发育树，ProPhylER 将其作为其数据流的一部分生成。路线、树和约束估计将通过将开发的网站上的图形界面提供。此外，由于 ProPhylER 的树提供了跨模型生物和基因组数据库关联蛋白质编码基因及其注释的自然框架，因此提出了与 SGD、Flybase 和 UCSC 浏览器的相互链接。我们预计ProPhylER将成为广泛使用的工具，用于分析相关基因之间的功能约束和系统发育关系。由于 ProPhylER 的数据是半自动生成的，并在数据流中的关键步骤进行管理，因此 ProPhylER 的数据具有高度的可靠性，对于研究特定蛋白质的个体研究人员来说很难重现。因此，最初它对实验者来说主要是有用的，对他们来说，约束分析可以指导结构功能分析，并且策划的比对和系统发育树将为他们提供感兴趣蛋白质的知识库。 ProPhylER 的扩展可对 cSNP 的有害性进行定量预测，从而将目标群体扩大到包括人类遗传学家和基因组学家。随着序列数据对大多数真核蛋白质的限制越来越少，ProPhylER 将扩展到覆盖大部分真核直向同源物空间，并成为通过进化关系将真核直向同源物和密切相关的旁系同源物联系在一起的数据库。