深度m5U:一种基于深度学习的方法,用于使用优化的特征集成来预测RNA5甲基尤里丁修饰
Sumaiya Noor1, Afshan Naseem2, Hamid Hussain Awan3
1Business and Management Sciences Department, Purdue University, West Lafayette, IN, USA.
BMC bioinformatics
|November 20, 2024
概括
使用混合方法,Deep-m5U准确地预测RNA5 - 甲基尤里丁 (m5U) 修饰. 这种计算生物学工具增强了m5U识别,比现有的转录和mRNA数据集模型提供更高的准确性.
科学领域:
- 计算生物学是一种计算生物学.
- 分子生物学分子生物学
- 生物信息学是一种生物信息学.
背景情况:
- RNA 5-甲基尤里丁 (m5U) 修改对生物功能至关重要.
- 在计算生物学中,准确识别m5U位点是必不可少的.
- 现有的m5U预测方法需要改进.
研究的目的:
- 介绍Deep-m5U,这是一个用于预测RNA m5U修改的新型计算工具.
- 为了提高m5U网站识别的准确性和可靠性.
- 为分子生物学和药物发现研究人员提供一个有价值的资源.
主要方法:
- 使用混合伪K双核酸组合 (PseKNC) 来进行序列表示.
- 在特征选择中使用了沙普利添加式扩展算法 (SHAP).
- 开发了一个用于预测的深度神经网络 (DNN) 分类器.
主要成果:
- 在基准数据集上,Deep-m5U实现了高精度:91.47% (完整转录) 和95.86% (成熟mRNA) 通过十倍的交叉验证.
- 独立样本测试的准确率为92.94% (完整转录) 和95.17% (成熟mRNA).
- 与现有模型相比,表现出优越的性能,训练数据的精度提高了5.23%,独立样本的精度提高了3.95%.
结论:
- 深m5U是RNA m5U修饰的可靠和有效预测器.
- 与当前方法相比,该模型提供了显著的精度改进.
- 深度m5U作为科学研究和制药开发的有价值的工具.
相关概念视频
02:23RNA Editing
8.9K
RNA editing is a post-transcriptional modification where a precursor mRNA (pre-mRNA) nucleotide sequence is changed by base insertion, deletion, or modification. The extent of RNA editing varies from a few hundred bases, in mitochondrial DNA of trypanosomes, to a just single base, in nuclear genes of mammals. Even a single base change in the pre-mRNA can convert a codon for one amino acid into the codon for another amino acid or a stop codon. This type of re-coding can significantly affect the...
8.9K
01:53RNA Stability
33.3K
Intact DNA strands can be found in fossils, while scientists sometimes struggle to keep RNA intact under laboratory conditions. The structural variations between RNA and DNA underlie the differences in their stability and longevity. Because DNA is double-stranded, it is inherently more stable. The single-stranded structure of RNA is less stable but also more flexible and can form weak internal bonds. Additionally, most RNAs in the cell are relatively short, while DNA can be up to 250 million...
33.3K
01:35Pre-mRNA Processing: Modification of pre-mRNA Ends
9.2K
In eukaryotic cells, transcripts made by RNA polymerase are modified and processed before exiting the nucleus. Unprocessed RNA is called precursor mRNA or pre-mRNA to distinguish it from mature mRNA.
Once about 20-40 ribonucleotides have been joined together by RNA polymerase, a group of enzymes adds a cap to the 5' end of the growing transcript. In this process, a 5' phosphate is replaced by modified guanosine that has a methyl group attached (7-methyl guanosine). This 5' cap helps...
Once about 20-40 ribonucleotides have been joined together by RNA polymerase, a group of enzymes adds a cap to the 5' end of the growing transcript. In this process, a 5' phosphate is replaced by modified guanosine that has a methyl group attached (7-methyl guanosine). This 5' cap helps...
9.2K
02:01pre-mRNA Processing
52.6K
In eukaryotic cells, transcripts made by RNA polymerase are modified and processed before exiting the nucleus. Unprocessed RNA is called precursor mRNA or pre-mRNA to distinguish it from mature mRNA.
Once about 20-40 ribonucleotides have been joined together by RNA polymerase, a group of enzymes adds a “cap” to the 5’ end of the growing transcript. In this process, a 5’ phosphate is replaced by modified guanosine that has a methyl group attached to it (7-Methyl...
Once about 20-40 ribonucleotides have been joined together by RNA polymerase, a group of enzymes adds a “cap” to the 5’ end of the growing transcript. In this process, a 5’ phosphate is replaced by modified guanosine that has a methyl group attached to it (7-Methyl...
52.6K