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贝格尔2.0:一种用于RNA二级结构的Web服务器,利用相似性检测,利用SHAPE指导的RNA结构确定

F Ballesio¹, A Teofani¹, C Carrino¹

¹Department of Biology, University of Rome "Tor Vergata", Rome, Italy.

Journal of molecular biology

|April 23, 2025

概括

BEAGLE 2.0 是一个调整RNA二次结构的Web服务器,可以在多种生物数据集中搜索结构相似性. 该工具有助于发现RNA同质性,并了解它们在生物过程中的作用.

科学领域:

生物信息学是一种生物信息学.
计算生物学计算生物学
分子生物学分子生物学

背景情况:

RNA二次结构在生物和病理过程中起着关键作用.
结构保护是识别单独通过序列分析遗漏的同质性的关键.
精确预测和对RNA二次结构的比较是必不可少的.

研究的目的:

介绍BEAGLE 2.0,一个增强的Web服务器,用于搜索RNA二级结构相似性.
促进用户提供的RNA分子和广泛的生物数据集之间的比较.
利用实验支持的数据来识别RNA中的结构相似性.

主要方法:

使用BEAGLE算法与BEAR编码,通过动态编程对对 RNA 二级结构进行对齐.
纳入各种数据集,包括SHAPE衍生结构 (人类,老鼠,斑马鱼,细菌,像SARS-CoV-2这样的病毒),NONCODE预测和基于Rfam的结构.
接受用户输入作为RNA序列或二次结构 (点括号或BEAR格式).

主要成果:

贝格尔2.0提供了与结构相似度和统计学意义的对齐.
以颜色编码元素提供RNA二次结构的视觉表示.
在大型,精心策划的RNA结构数据集中实现高效的搜索.

结论:

贝格尔2.0显著扩大了RNA二次结构比较的能力.
使用多样化,经过实验验证的数据集,方便发现功能性RNA相似性.
为研究RNA功能和进化研究的研究人员提供了宝贵的资源.

关键词:

检测RNA同质性的检测RNA同质性的检测配对RNA二级结构的调整搜索RNA结构相似性的搜索在icSHAPE数据集成中,数据集成非编码RNAs (ncRNAs) 是一种非编码RNA.

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