Computational Prediction of RNA Viral Genome Structures
RNA病毒基因组结构的计算预测
基本信息
- 批准号:7858089
- 负责人:
- 金额:$ 14.72万
- 依托单位:
- 依托单位国家:美国
- 项目类别:
- 财政年份:
- 资助国家:美国
- 起止时间:至
- 项目状态:未结题
- 来源:
- 关键词:AlgorithmsAntiviral AgentsBase SequenceBioinformaticsBirdsCommunitiesComputer softwareComputersCoronavirusCross InfectionDevelopmentDisease OutbreaksElementsEnvironmentEvolutionGene ExpressionGenomeGenomicsGoalsImmune responseIncidenceIndividualInfectionInfluenzaInternationalInternetInvestigationLengthLocationMutateProductionProteinsRNARNA VirusesReading FramesReportingReproductionResearch PersonnelRiskSevere Acute Respiratory SyndromeStructureSystemTechnologyTestingTexasTimeUniversitiesVariantViralViral GenomeVirusVirus DiseasesWood materialbasecluster computingcombatcomputerized toolsdesigngenome sequencinginfluenzavirusopen sourcepandemic diseaseprogramsprototyperesearch studystatisticsstemtooluser-friendlyvirus pathogenesis
项目摘要
The genomes of some pathogenic viruses are made up of RNA that can be involved directly in the
production of proteins crucial to viral reproduction and infection. These fast-mutating RNA viruses showed a
high incidence of cross-infections among different species by variant forms (Plant et al. 2005). It is feasible to
perform computational analyses on the viral genome and obtain useful information which give clues to the
origin, natural reservoir, and evolution of the virus, contributing to the understanding of the immune response
to these viruses and the pathogenesis of viral diseases and facilitate the development of antiviral drugs. We
have recently reported that regions in coronavirus RNA genomes with statistically significant clusters of
palindromes are associated with the presence of stem-loops or pseudoknots (Chew et al 2004). These RNA
structures have been suggested to be responsible for frame-shifting mechanisms during gene expression,
where two different proteins can be produced in the same region just by shifting the reading frame by one
base. We hypothesize that by exploiting the correlation between nonrandom clusters of close inversions with
stem-loop and pseudoknot structures in RNA molecules, an efficient and utilitarian tool for predicting
secondary structures on RNA viral genomes can be developed using current heterogeneous Grid Computing
technology. We propose a four-year project to evaluate this hypothesis focusing on coronaviruses and
influenza viruses with specific aims to: (1) Establish a statistics-based algorithm to locate RNA segment
containing nonrandom clusters of close inversions. (2) Develop a strategy for cutting of the viral genome
sequences into segments of length no greater than 200 bases. (3) Construct a software prototype for RNA
secondary structure prediction using Grid Computing technology. (4) Implement user facilities for the
software and predict genome structures in coronaviruses and Influenza viruses. For this project, our
objective is to produce the prototype of an RNA secondary structure prediction system on a grid of
heterogeneous, distributed computers. The software will be publicly accessible through a web portal. Our
long-term goal is to develop a set of open-source computational tools in a Grid Computing environment to
accurately predict genome structures and dynamics in RNA viruses and their interactions with cellular RNA.
This will provide information to be used by virologists to design finely tuned experiments to study RNA
viruses and their pathogenic interactions with their hosts, especially when time is limiting in combating new infectious viral diseases.
一些致病病毒的基因组由RNA组成,它可以直接参与病毒的
产生对病毒繁殖和感染至关重要的蛋白质。这些快速变异的RNA病毒显示出
不同物种之间通过变异形式交叉感染的高发生率(Factory等人。2005)。这是可行的
对病毒基因组进行计算分析,并获得有用的信息,为
病毒的起源、自然储存库和进化,有助于了解免疫反应
为这些病毒和病毒性疾病的发病机制及抗病毒药物的开发提供便利。我们
最近报道了冠状病毒RNA基因组中具有统计意义的聚集簇的区域
回文与茎环或伪节的存在有关(Chew等人,2004年)。这些RNA
结构被认为在基因表达过程中负责移帧机制,
只需将阅读框移动一位,就可以在同一区域产生两种不同的蛋白质
基地。我们假设,通过利用非随机的近倒数簇之间的相关性
RNA分子中的茎环和伪结结构--一种有效和实用的预测工具
利用当前的异质网格计算可以开发RNA病毒基因组上的二级结构
技术我们提出了一个为期四年的项目来评估这一假设,重点是冠状病毒和
流感病毒的具体目标是:(1)建立基于统计的算法来定位RNA片段
包含非随机的紧密倒置的簇。(2)制定病毒基因组切割策略
序列分成长度不超过200个碱基的片段。(3)构建了RNA的软件原型
利用网格计算技术进行二级结构预测。(4)为用户提供便利
软件和预测冠状病毒和流感病毒的基因组结构。对于这个项目,我们的
目标是在网格上产生RNA二级结构预测系统的原型
异类、分布式计算机。该软件将通过一个门户网站向公众开放。我们的
长期目标是在网格计算环境中开发一组开源计算工具,以
准确预测RNA病毒的基因组结构和动态,以及它们与细胞RNA的相互作用。
这将为病毒学家设计精心调整的实验以研究RNA提供信息
病毒及其与宿主的致病相互作用,特别是在抗击新的传染性病毒疾病的时间有限的情况下。
项目成果
期刊论文数量(0)
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会议论文数量(0)
专利数量(0)
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{{ truncateString('MING-YING LEUNG', 18)}}的其他基金
Computational Prediction of RNA Viral Genome Structures
RNA病毒基因组结构的计算预测
- 批准号:
7282250 - 财政年份:2007
- 资助金额:
$ 14.72万 - 项目类别:
Computational Prediction of RNA Viral Genome Structures
RNA病毒基因组结构的计算预测
- 批准号:
8080329 - 财政年份:
- 资助金额:
$ 14.72万 - 项目类别:
Computational Prediction of RNA Viral Genome Structures
RNA病毒基因组结构的计算预测
- 批准号:
7617072 - 财政年份:
- 资助金额:
$ 14.72万 - 项目类别:
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