The ProPhylER Database and Web Resource

ProPhylER 数据库和网络资源

• 批准号: 6710959
• 负责人: AREND SIDOW
• 金额: $ 46.76万
• 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 2007-08-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/6710959
• 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）： 我们建议将Prophyler（蛋白质系统发育和进化率）数据库作为通用研究界可用的网络资源。 Prophyler数据库将对直系同源物和密切相关的旁系同源物的局部约束进行定量估计。约束的估计需要健壮，策划，比对和系统发育树，这些树是其数据流的一部分产生的。将通过将要开发的网站上的图形接口提供约束的对齐，树和估计值。此外，由于Prophyler的树提供了与模型生物体和基因组数据库之间蛋白质编码基因及其注释相关的自然框架，因此提出了与SGD，FlyBase和UCSC浏览器的相互链接。我们预计，Prophyler将成为一种广泛使用的工具，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的数据是在数据流中的关键步骤下进行半毒性生成的，因此Prophyler的数据具有高度的可靠性，对于从事特定蛋白质的个体研究人员来说，很难再现。因此，最初，它主要对于实验学家的约束分析可以指导结构函数分析，并且为之指导的结构函数分析，并且为之策划的比对和系统发育树将为感兴趣的蛋白质提供知识库。 prophyler的扩展以产生CSNP的有害性的定量预测，将扩大目标群落，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的限制越来越少，Prophyler将扩展以覆盖大多数真核直源性直立空间，并成为通过其进化关系将真核生物正交类和紧密相关的旁系同源物联系在一起的数据库。