A Flexible and Efficient System for the Detection of RNA Sequence/Structure Motifs
用于检测 RNA 序列/结构基序的灵活高效的系统
基本信息
- 批准号:110058642
- 负责人:
- 金额:--
- 依托单位:
- 依托单位国家:德国
- 项目类别:Research Grants
- 财政年份:2009
- 资助国家:德国
- 起止时间:2008-12-31 至 2021-12-31
- 项目状态:已结题
- 来源:
- 关键词:
项目摘要
Non-coding RNAs (ncRNAs) are involved in many regulatory processes of a cell. An overwhelming number of ncRNAs is found by whole transcriptome analyses (next-generation-sequencing (NGS)), most of which are not annotated. The functional analysis of ncRNA relies heavily on sequence-structure similarities. Due to the high computational complexity, however, tools for finding sequence-structure similarities are currently not used for annotating newly identified ncRNA. Current computational genome-wide ncRNA analysis often consumes enormous computing resources (ten to hundreds of computer years). Our goal is to setup a system for analyzing and annotating ncRNAs that consists of a set of efficient algorithms and tools for detecting sequence-structure similarity. We will provide an easy-to-use web-based interface to allow biologists to perform ncRNA annotation tasks, and to analyze the ncRNA in its genomic context using personalized genome browser tracks. The combined system will allow two major tasks to be performed: 1.) To search for annotated ncRNAs or ncRNA transcripts in other NGS data or in ncRNA databases that have structural similarity for a newly detected ncRNAs. We will consider both structured small ncRNAs as well as long non-coding RNAs (lncRNA), where globally conserved structure has not been found yet. 2.) To cluster a set of new non-coding RNAs in order to determine structural classes, which is a prerequisite for functional annotation of new ncRNA classes. In particular, this involves a global clustering of complete transcripts. We will also work on the problem of local clustering, based on local alignments, to find regulatory motifs that are embedded into longer transcripts (e.g., cis-regulatory elements like the IRE (iron response element), IRES (internal ribosome entry site) etc.). This problem is currently hard to solve using automated tools. Our first major objective is to directly improve the efficiency and quality of our sequence-structure alignment approach by using advanced algorithmic techniques. Currently, the best exact algorithmic approaches are not efficient enough for routinely scanning for hundreds (if not thousands) of ncRNAs, typically found in transcriptome data. To make our tools applicable in practice, and thus to fullfill the needs of our cooperation partners, we have to design fast and sensitive filters in order to significantly reduce the number of expensive sequencestructure comparisons. Previous approaches used sequence-based filtering. Obviously, this filtering only works for ncRNAs with high sequence similarities. It is known, however, that conserved ncRNAs may have a very low sequence conservation. Therefore, our second major objective is to develop fast sequencestructure-based filtering methods based on our efficient graph-kernel approach.
非编码RNA(ncRNA)参与细胞的许多调控过程。通过全转录组分析(下一代测序(NGS))发现了压倒性数量的ncRNA,其中大多数未被注释。ncRNA的功能分析在很大程度上依赖于序列结构相似性。然而,由于高计算复杂性,用于寻找序列结构相似性的工具目前不用于注释新鉴定的ncRNA。目前的计算全基因组ncRNA分析通常消耗巨大的计算资源(十到数百个计算机年)。我们的目标是建立一个分析和注释ncRNA的系统,包括一套有效的算法和工具,用于检测序列结构相似性。我们将提供一个易于使用的基于网络的界面,让生物学家执行ncRNA注释任务,并分析ncRNA在其基因组背景下使用个性化的基因组浏览器跟踪。合并后的系统将允许执行两项主要任务:1。在其他NGS数据或ncRNA数据库中搜索与新检测到的ncRNA具有结构相似性的注释ncRNA或ncRNA转录本。我们将考虑结构化的小ncRNA以及长非编码RNA(lncRNA),其中尚未发现全局保守的结构。2.)的情况。对一组新的非编码RNA进行聚类,以确定结构类别,这是对新的ncRNA类别进行功能注释的先决条件。特别是,这涉及完整转录本的全局聚类。我们还将研究基于局部比对的局部聚类问题,以找到嵌入较长转录本的调控基序(例如,顺式调节元件如IRE(铁反应元件)、IRES(内部核糖体进入位点)等)。这个问题目前很难用自动化工具来解决。我们的第一个主要目标是通过使用先进的算法技术直接提高我们的序列结构比对方法的效率和质量。目前,最好的精确算法方法对于通常在转录组数据中发现的数百(如果不是数千)ncRNA的常规扫描不够有效。为了使我们的工具在实践中适用,从而满足我们的合作伙伴的需求,我们必须设计快速和灵敏的过滤器,以显着减少昂贵的sequencestructure比较的数量。以前的方法使用基于序列的过滤。显然,这种过滤仅适用于具有高序列相似性的ncRNA。然而,已知保守的ncRNA可能具有非常低的序列保守性。因此,我们的第二个主要目标是开发快速sequencestructure-based过滤方法的基础上,我们的高效的图形内核的方法。
项目成果
期刊论文数量(10)
专著数量(0)
科研奖励数量(0)
会议论文数量(0)
专利数量(0)
RNAscClust: clustering RNA sequences using structure conservation and graph based motifs
- DOI:10.1093/bioinformatics/btx114
- 发表时间:2017-07-15
- 期刊:
- 影响因子:5.8
- 作者:Miladi, Milad;Junge, Alexander;Backofen, Rolf
- 通讯作者:Backofen, Rolf
Local Exact Pattern Matching for Non-Fixed RNA Structures
- DOI:10.1109/tcbb.2013.2297113
- 发表时间:2014-01-01
- 期刊:
- 影响因子:4.5
- 作者:Amit, Mika;Backofen, Rolf;Will, Sebastian
- 通讯作者:Will, Sebastian
ExpaRNA-P: simultaneous exact pattern matching and folding of RNAs
- DOI:10.1186/s12859-014-0404-0
- 发表时间:2014-12-31
- 期刊:
- 影响因子:3
- 作者:Otto, Christina;Moehl, Mathias;Will, Sebastian
- 通讯作者:Will, Sebastian
Fast and Accurate Structure Probability Estimation for Simultaneous Alignment and Folding of RNAs
快速准确地估计 RNA 同时比对和折叠的结构概率
- DOI:10.4230/lipics.wabi.2019.14
- 发表时间:2019
- 期刊:
- 影响因子:0
- 作者:Milad Miladi;Martin Raden;Sebastian Will;Rolf Backofen
- 通讯作者:Rolf Backofen
MutaRNA: analysis and visualization of mutation-induced changes in RNA structure
MutaRNA:突变引起的 RNA 结构变化的分析和可视化
- DOI:10.1093/nar/gkaa331
- 发表时间:2020
- 期刊:
- 影响因子:14.9
- 作者:Milad Miladi;Martin Raden;Sven Diederichs;Rolf Backofen
- 通讯作者:Rolf Backofen
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Professor Dr. Rolf Backofen其他文献
Professor Dr. Rolf Backofen的其他文献
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{{ truncateString('Professor Dr. Rolf Backofen', 18)}}的其他基金
Prediction of RNA-RNA Interactions by Kinetic Modelling
通过动力学模型预测 RNA-RNA 相互作用
- 批准号:
312982092 - 财政年份:2016
- 资助金额:
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Research Grants
The population genetics of the CRISPR-Cas system in bacteria
细菌 CRISPR-Cas 系统的群体遗传学
- 批准号:
285672682 - 财政年份:2015
- 资助金额:
-- - 项目类别:
Priority Programmes
eCLASH Towards defining the small RNA interactome
eCLASH 致力于定义小 RNA 相互作用组
- 批准号:
286021192 - 财政年份:2015
- 资助金额:
-- - 项目类别:
Research Grants
Functional characterisation of the non-coding RNA Pantr1 in FOXG1-dependent forebrain development and Rett-syndrome
FOXG1 依赖性前脑发育和 Rett 综合征中非编码 RNA Pantr1 的功能特征
- 批准号:
255240006 - 财政年份:2014
- 资助金额:
-- - 项目类别:
Priority Programmes
ATP - Automated Intra-Annual Tree-Ring Profiling for Dendroecological Research
ATP - 用于树木生态学研究的自动年轮分析
- 批准号:
269191667 - 财政年份:2014
- 资助金额:
-- - 项目类别:
Research Grants
Bioinformatic analyses of CRISPR elements
CRISPR元件的生物信息分析
- 批准号:
206968047 - 财政年份:2011
- 资助金额:
-- - 项目类别:
Research Units
MiRNA and RNA-binding proteins as integral part of cell communication:context-based target prediction and validation
miRNA 和 RNA 结合蛋白作为细胞通讯的组成部分:基于上下文的目标预测和验证
- 批准号:
151246655 - 财政年份:2010
- 资助金额:
-- - 项目类别:
Priority Programmes
Computational Detection of Bacterial ncRNAs and their Targets
细菌 ncRNA 及其靶标的计算检测
- 批准号:
39932908 - 财政年份:2007
- 资助金额:
-- - 项目类别:
Priority Programmes
Algorithmic determination of whether a protein`s cysteine residue can be replaced by selenocysteine by silent/similiar pointwise mutagenesis in DNA/RNA. Intended application to phase determination in X-ray crystallography and NMR spectroscopy.
通过 DNA/RNA 中的沉默/类似逐点诱变,算法确定蛋白质的半胱氨酸残基是否可以被硒代半胱氨酸取代。
- 批准号:
5241840 - 财政年份:2000
- 资助金额:
-- - 项目类别:
Priority Programmes
Service Project: "CRISPR Bioinformatics"
服务项目:“CRISPR生物信息学”
- 批准号:
405939317 - 财政年份:
- 资助金额:
-- - 项目类别:
Priority Programmes
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