HyPhy: Molecular Evolutionary Analyses

HyPhy：分子进化分析

• 批准号: 8143338
• 负责人: Spencer V. Muse
• 金额: $ 27.57万
• 依托单位: NORTH CAROLINA STATE UNIVERSITY RALEIGH
• 依托单位国家: 美国
• 财政年份: 2010
• 资助国家: 美国
• 起止时间: 2010-09-15 至 2014-08-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/8143338
• 关键词: Amino Acids; Animal Model; Area; Biomedical Research; Book Chapters; Classification; Code; Codon Nucleotides; Collection; Computer software; DNA; Data; Data Analyses; Development; Documentation; Drug resistance; Evolution; Funding; Gene Mutation; Genes; Genetic Programming; Genome; Genomics; Goals; Human; Immune response; Internet; Language; Libraries; Likelihood Functions; Machine Learning; Maintenance; Modeling; Molecular; Molecular Evolution; Molecular Sequence Data; Online Systems; Pathogenicity; Pattern; Peer Review; Performance; Phylogenetic Analysis; Phylogeny; Population; Procedures; Publications; RNA; Research Personnel; Resources; Software Engineering; Study models; System; Testing; Viral; Work; acronyms; base; combinatorial; comparative genomics; design; flexibility; improved; pathogen; pressure; programs; protein structure function; public health relevance; research study; tool; user-friendly; wiki

DESCRIPTION (provided by applicant): Project Description HyPhy (http://www.hyphy.org) is a scriptable software platform designed to enable flexible and powerful analyses of DNA, RNA, codon, amino acid and other types of sequence data in an evolutionary context. Such analyses have become an indispensable component of most research studies that make use of comparative genomic data. Biologists and bioinformaticians increasingly recognize the benefits of molecular evolutionary analyses. Since its initial release in 2001, HyPhy has become a relatively stable and mature product, and has been downloaded by more than 4,500 unique users, integrated into several popular web-based genomic data analysis servers, cited in over 400 peer-reviewed publications and described in three book chapters, in spite of the fact that the development of the package has never been directly funded. This proposal seeks support to improve the quality, performance, reliability, modularity, documentation and feature sets of the HyPhy system. Specific aims can be divided into four major areas: 1. Software engineering, testing, and documentation of the HyPhy codebase. 2. The development of a high-performance engine for phylogenetic maximum likelihood model fitting and inference. 3. Extension of a newly-initiated toolbox for machine learning applications in molecular evolution. 4. Creation and maintenance of a wiki-themed documentation resource. PUBLIC HEALTH RELEVANCE: Project Narrative Molecular evolutionary analyses are central to many aspects of basic, translational, and applied biomedical research. Examples include identifying gene mutations that allow pathogens to evade the immune response; prediction of the structure and function of proteins; estimating the evolutionary relatedness of human or other populations; characterizing the magnitude of selective pressure, either natural or artificial, on genes or species.

描述（由申请人提供）：项目描述HyPhy（http：www.hyphy.org）是一个可编写脚本的软件平台，设计用于在进化背景下对DNA、RNA、密码子、氨基酸和其他类型的序列数据进行灵活而强大的分析。这种分析已成为大多数利用比较基因组数据的研究的不可或缺的组成部分。生物学家和生物信息学家越来越认识到分子进化分析的好处。自2001年首次发布以来，HyPhy已成为一个相对稳定和成熟的产品，并已被4，500多个独立用户下载，集成到几个流行的基于网络的基因组数据分析服务器中，在400多个同行评审的出版物中引用，并在三个章节中描述，尽管该软件包的开发从未得到直接资助。该提案寻求支持，以改进HyPhy系统的质量、性能、可靠性、模块化、文档和功能集。具体目标可分为四大方面：1. HyPhy代码库的软件工程、测试和文档编制。2.开发一个高性能的系统发育最大似然模型拟合和推理引擎。3.扩展新启动的工具箱，用于分子进化中的机器学习应用。4.创建和维护维基主题的文档资源。 公共卫生关系：分子进化分析是基础、转化和应用生物医学研究的许多方面的核心。例子包括识别允许病原体逃避免疫反应的基因突变;预测蛋白质的结构和功能;估计人类或其他群体的进化相关性;表征基因或物种上自然或人为的选择压力的大小。