An all-in-one web server for RNA structure prediction using evolutionary information

一种使用进化信息预测 RNA 结构的一体化网络服务器

基本信息

  • 批准号:
    10574944
  • 负责人:
  • 金额:
    $ 24.99万
  • 依托单位:
  • 依托单位国家:
    美国
  • 项目类别:
  • 财政年份:
    2023
  • 资助国家:
    美国
  • 起止时间:
    2023-01-01 至 2024-12-31
  • 项目状态:
    已结题

项目摘要

Project Abstract RNA structure and function are intimately linked. To sort out what the myriad RNAs in transcriptomes are doing, we need rigorous approaches that also infer structure. Many predictive algorithms already exist, but they output models for any and every sequence, and different approaches often output different models for the same sequence. This results in suboptimal models that permeate the field, and in ascribing structure to RNAs that don't in fact have any conserved structure. What the field of RNA research needs now to go forward is a computational tool that will evaluate the likelihood that a certain RNA sequence has a biological structure, and propose that structure with the highest accuracy. The best approach to this issue has been for a long time the comparison of homologous sequences from diverse organisms. This same approach is actually at the basis of the most successful protein structure prediction tools. But a hindrance in the wide adoption of such approaches for predicting RNA structure is that sequence comparison requires knowledge and expertise in computational and structural biology as well as access to tools that are not mainstream. This proposal is about the development of a freely available webserver for reliably predicting RNA secondary and eventually tertiary structures using evolutionary information. This webserver will operate behind the scenes as a suite of tools (the outputs of which will be available for interested users), from homologous sequences retrieval to evaluation of the resulting model. First, this tool will automatically retrieve and align homologous sequences using existing and novel algorithms. This aim will search for relevant homologs to any single sequence entered as input, which represents an unmet challenge for most current programs. Second, the application using covariation analysis will address the likeliness that the input RNA sequence has a conserved structure, so not every sequence used as input will necessarily output a structure model. Subsequent modules in the online tool will evaluate the quality of the alignment, and possibly improve this alignment, so that a model with a confidence score could be proposed. Regardless of the outcome, the user will have a result that will take into account evolutionary as well as up-to-date RNA structural information, so it will not be biased by the use of a single set of parameters, as is often the case with existing predictive methods. A more holistic and straightforward computational tool harnessing evolutionary information will help disseminate the use of those methods to the larger RNA biology community, for maximum impact on experimental design in RNA research.
项目摘要

项目成果

期刊论文数量(0)
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Elena Rivas其他文献

Elena Rivas的其他文献

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{{ truncateString('Elena Rivas', 18)}}的其他基金

Discovery of structural RNAs involved in human health and disease
发现与人类健康和疾病有关的结构RNA
  • 批准号:
    10704745
  • 财政年份:
    2022
  • 资助金额:
    $ 24.99万
  • 项目类别:
Computational approaches to noncoding RNAs
非编码 RNA 的计算方法
  • 批准号:
    7059274
  • 财政年份:
    2006
  • 资助金额:
    $ 24.99万
  • 项目类别:
Computational methods to identify noncoding RNA genes
识别非编码 RNA 基因的计算方法
  • 批准号:
    7025050
  • 财政年份:
    2005
  • 资助金额:
    $ 24.99万
  • 项目类别:
Computational methods to identify noncoding RNA genes
识别非编码 RNA 基因的计算方法
  • 批准号:
    6869927
  • 财政年份:
    2005
  • 资助金额:
    $ 24.99万
  • 项目类别:
Regulatory and functional RNAs: computational approaches
调控和功能 RNA:计算方法
  • 批准号:
    6687991
  • 财政年份:
    2003
  • 资助金额:
    $ 24.99万
  • 项目类别:
Probabilistic methods to identify noncoding RNA genes
鉴定非编码 RNA 基因的概率方法
  • 批准号:
    6536488
  • 财政年份:
    2001
  • 资助金额:
    $ 24.99万
  • 项目类别:
Probabilistic methods to identify noncoding RNA genes
鉴定非编码 RNA 基因的概率方法
  • 批准号:
    6321572
  • 财政年份:
    2001
  • 资助金额:
    $ 24.99万
  • 项目类别:
Probabilistic methods to identify noncoding RNA genes
鉴定非编码 RNA 基因的概率方法
  • 批准号:
    6638074
  • 财政年份:
    2001
  • 资助金额:
    $ 24.99万
  • 项目类别:

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