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CircCode3:集成深度学习来挖掘和评估可翻译的圆形RNA,这些RNA来自于核糖体分析测序和质谱数据

Zonghui Zhu¹, Xiaojuan Liang¹, Rui Ma¹

¹Key Laboratory of Ministry of Education for Medicinal Plant Resource and Natural Pharmaceutical Chemistry, National Engineering Laboratory for Resource Development of Endangered Crude Drugs in Northwest China, College of Life Sciences, Shaanxi Normal University, Xi'an, Shaanxi 710119, China.

Briefings in bioinformatics

|September 18, 2025

概括

识别可翻译的循环RNA (circRNAs) 和它们的开放式读取框架 (ORFs) 是一个挑战. CircCode3是一个新的管道,集成工具来准确地从测序数据中挖掘和评估可翻译的circRNA.

科学领域:

分子生物学分子生物学
生物信息学是一种生物信息学.
基因组学就是基因组学.

背景情况:

循环RNAs (circRNAs) 可以通过独立于帽的翻译来编码蛋白质/.
机制包括m6A修饰和内部核糖体进入部位 (IRES) 启动.
准确识别可翻译的circRNA及其开放的读取框架 (ORF) 仍然是一个挑战.

研究的目的:

开发一个综合分析管道,CircCode3,用于挖掘可翻译的circRNAs.
加强circRNAORF的识别和评估,包括跨越背接接口的ORF.
整合用于评估IRES潜力和预测m6A修改站点的工具.

主要方法:

开发CircCode3集成分析管道.
整合IRESfinder用于IRES潜在评估.
开发DeepCircm6A用于m6A位点预测和DLMSC用于停止编码子可靠性评估.
对核糖体分析和质谱学数据的分析.

主要成果:

CircCode3提供了增强的功能,用于从高通量测序数据中挖掘可翻译的circRNA.
管道准确地识别和评估ORF,包括跨越背接接口的ORF.
深度学习工具提高了监管元素 (m6A) 和翻译终止 (停止编码子) 的预测.

结论:

CircCode3为分析circRNA翻译提供了一个全面的解决方案.
该管道有助于识别和评估可翻译的circRNA及其ORF.
为了推进circRNA研究,CircCode3是公开的.

关键词:

圆形的RNAs是圆形的RNAs.质谱测量质谱测量质谱测量质谱测量质量测量质谱测量质量测量质量测量质量测量质量测量质量测量质量测量质量测量质量测量质量测量质量测量质量测量质量测量质量测量质量测量质量测量质量测量质量测量质量测量质量测量核糖体造型测序序列的排序.可以翻译的circRNAs

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