权益分类	功能权益	普通用户	{{item.name}}会员
{{category.name}}	{{benefitItem.name}}

PRPTree: Novel bioinformatics software for improved understanding of the temporal context of evolutionary divergence

PRPTree：新型生物信息学软件，可提高对进化分歧时间背景的理解

基本信息

批准号：
BB/S019952/1
负责人：
Mark Pagel
金额：
$ 46.9万
依托单位：
University of Reading
依托单位国家：
英国
项目类别：
Research Grant
财政年份：
2020
资助国家：
英国
起止时间：
2020 至无数据
项目状态：
已结题

来源：
https://gtr.ukri.org/projects?ref=BB%2FS019952%2F1
关键词：
PRPTree Novel bioinformatics software improved

项目摘要

In the life sciences, the field of bioinformatics is concerned with compiling large databases of information on organisms - such as DNA or gene sequences - and with developing methods for analysing those databases. Because all living things are connected to each other by their common ancestry, one of the most common bioinformatics tasks is to develop an evolutionary tree or 'phylogeny' of a group of species. A phylogeny is like a family tree but traces the historical lines of descent from older to younger species rather than from parents to their offspring. Scientists reconstruct them by studying the similarities and differences among species in their DNA sequences. They then use the phylogenies to describe the probable course of evolution over millions of years, to see how species evolve and adapt, to study the ways genes and proteins evolve and to reconstruct the timings and pace of change of past events. The Principal Investigator of this project has derived a new statistical method that can potentially greatly improve our ability to estimate the dates and timings of past events of evolution on phylogenetic trees. The proposed research is to i) implement and test this new method, ii) to compile a database of the rates at which species evolve and iii) to make the new method and the database available to others as an easy-to-use bioinformatics tool. Regarding the first goal, the new method we will develop improves our ability to estimate the timings of past events of evolution by allowing investigators to measure more accurately the rate or speed with which DNA sequences acquire differences. This improved dating makes the phylogenies more useful for scientific research. In turn, improved phylogenies will allow scientists to provide better answers to questions like when did the ancestor to humans and chimpanzees live? Or when and where did the Zika or Ebola viruses emerge? The second goal of our work is to compile a database of the rates of evolution observed across a variety of species including plants, animals, bacteria and viruses. Our preliminary work suggests that some extraordinarily highly elevated rates of evolution can occur - 10 or more times the background rate. Knowledge of these rates is important for dating phylogenies, but also for understanding questions like how quickly can bacteria acquire resistance to antibiotics, or viruses outwit our immune systems or whether species can evolve fast enough to respond to climate change.Our third goal is to make our new method freely available to other researchers as a bioinformatics tool known as PRPTree. We produce a software package, as do several other groups, for inferring phylogenetic trees, and we will share our methods with those other developers.

在生命科学中，生物信息学领域涉及汇编关于生物体的大型信息数据库-如DNA或基因序列-并开发分析这些数据库的方法。由于所有生物都通过其共同的祖先相互联系，因此最常见的生物信息学任务之一是开发一组物种的进化树或“进化史”。一个谱系就像一个家谱，但追溯的历史线的后裔从老到年轻的物种，而不是从父母到他们的后代。科学家们通过研究物种DNA序列的相似性和差异来重建它们。然后，他们使用遗传学来描述数百万年来可能的进化过程，观察物种如何进化和适应，研究基因和蛋白质进化的方式，并重建过去事件的时间和变化速度。该项目的主要研究者已经得出了一种新的统计方法，可以大大提高我们在系统发育树上估计过去进化事件的日期和时间的能力。拟议的研究是i）实施和测试这种新方法，ii）编制物种进化速率的数据库，iii）将新方法和数据库作为易于使用的生物信息学工具提供给其他人。关于第一个目标，我们将开发的新方法通过允许研究人员更准确地测量DNA序列获得差异的速率或速度来提高我们估计过去进化事件的时间的能力。这种改进的测年方法使生物钟对科学研究更有用。反过来，改进的遗传学将使科学家能够更好地回答诸如人类和黑猩猩的祖先生活在什么时候之类的问题。寨卡病毒或埃博拉病毒是何时何地出现的？我们工作的第二个目标是编制一个数据库，记录在包括植物、动物、细菌和病毒在内的各种物种中观察到的进化速率。我们的初步工作表明，一些非常高的进化速度可能会发生- 10倍或更多的背景速度。了解这些速率对于确定细菌的遗传时间很重要，但对于理解细菌对抗生素的耐药性有多快，病毒对我们的免疫系统有多聪明，或者物种是否能进化得足够快以应对气候变化等问题也很重要。我们的第三个目标是将我们的新方法免费提供给其他研究人员，作为一种名为PRPTree的生物信息学工具。我们制作了一个软件包，就像其他几个小组一样，用于推断系统发育树，我们将与其他开发人员分享我们的方法。