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ABI Innovation: Identifying phylogenetically informative data from next-generation sequencing

ABI 创新：从下一代测序中识别系统发育信息数据

基本信息

批准号：
1356548
负责人：
Reed Cartwright
金额：
$ 68.62万
依托单位：
Arizona State University
依托单位国家：
美国
项目类别：
Standard Grant
财政年份：
2014
资助国家：
美国
起止时间：
2014-08-01 至 2018-07-31
项目状态：
已结题

来源：
https://www.nsf.gov/awardsearch/showAward?AWD_ID=1356548&HistoricalAwards=false
关键词：
ABI Innovation Identifying phylogenetically informative

项目摘要

Knowledge of evolutionary relationships among species forms the fundamental basis for research in fields ranging from agriculture to ecology to medicine. This project aims to develop new methods and software to rapidly process large genomic datasets and extract information that helps improve our understanding of these relationships. This project will provide extensive bioinformatics training for 3-6undergraduates; computer exercises will be developed to engage hundreds of additional undergraduates in college courses. Research updates and explanations will be provided to the scientific community at annual conferences, and to the general public through the popular science weblog, The Panda?s Thumb (http://www.pandasthumb.org/).This research seeks to develop software that will facilitate numerous projects in the field of evolution, including research on non-model organisms and emerging infectious diseases. First, this research will produce a method to identify regions of the genome that are similar enough that they can be compared among diverse groups. Second, new statistical models will be developed to accurately determine the sequence for each species for these regions given the error in current methods of genome sequencing. Third, methods will be developed to automate the identification of data that is useful to determine both recent and ancient evolutionary events. The resulting data can be used in established analytical software platforms. The methods developed by this project will be made available to the scientific community as robust, easy-to-use software at https://github.com/rachelss/SISRS.

对物种间进化关系的了解构成了农业、生态学和医学等领域研究的基础。该项目旨在开发新的方法和软件来快速处理大型基因组数据集并提取有助于提高我们对这些关系的理解的信息。该项目将为3-6名本科生提供广泛的生物信息学培训；将开发计算机练习，以吸引数百名本科生参加大学课程。研究更新和解释将在年度会议上向科学界提供，并通过科普博客 The Panda?s Thumb (http://www.pandasthumb.org/) 向公众提供。这项研究旨在开发软件，以促进进化领域的众多项目，包括对非模式生物和新出现的传染病的研究。首先，这项研究将产生一种方法来识别基因组中足够相似的区域，以便可以在不同群体之间进行比较。其次，考虑到当前基因组测序方法的错误，将开发新的统计模型来准确确定这些区域的每个物种的序列。第三，将开发自动识别数据的方法，这些数据有助于确定最近和古代的进化事件。所得数据可用于已建立的分析软件平台。该项目开发的方法将作为强大且易于使用的软件提供给科学界：https://github.com/rachelss/SISRS。