Reconstruction of Full-Length circRNA Sequences Using Chimeric Alignment Information

doi:10.3390/ijms23126776

	Reconstruction of Full-Length circRNA Sequences Using Chimeric Alignment Information
	Hossain, Md. Tofazzal 1,2,3; Zhang, Jingjing 1,2; Reza, Md. Selim 1,2; Peng, Yin 4; Feng, Shengzhong 1; Wei, Yanjie 1
	2022-06-01
发表期刊	INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
卷号	23 期号:12 页码:15
摘要	Circular RNAs (circRNAs) are RNA molecules formed by joining a downstream 3 splice donor site and an upstream 5 splice acceptor site. Several recent studies have identified circRNAs as potential biomarker for different diseases. A number of methods are available for the identification of circRNAs. The circRNA identification methods cannot provide full-length sequences. Reconstruction of the full-length sequences is crucial for the downstream analyses of circRNA research including differential expression analysis, circRNA-miRNA interaction analysis and other functional studies of the circRNAs. However, a limited number of methods are available in the literature for the reconstruction of full-length circRNA sequences. We developed a new method, circRNA-full, for full-length circRNA sequence reconstruction utilizing chimeric alignment information from the STAR aligner. To evaluate our method, we used full-length circRNA sequences produced by isocirc and ciri-long using long-reads RNA-seq data. Our method achieved better reconstruction rate, precision, sensitivity and F1 score than the existing full-length circRNA sequence reconstruction tool ciri-full for both human and mouse data.
关键词	circular RNA reconstruction of circRNA sequence full-length sequence
DOI	10.3390/ijms23126776
收录类别	SCI
语种	英语
资助项目	National Key Research and Development Program of China[2018YFB0204403] ; key Research and Development Project of Guangdong Province[2021B0101310002] ; Strategic Priority CAS Project[XDB38050100] ; National Science Foundation of China[U1813203] ; Shenzhen Basic Research Fund[RCYX2020071411473419] ; Shenzhen Basic Research Fund[KQTD20200820113106007] ; Shenzhen Basic Research Fund[JSGG20201102163800001] ; CAS Key Lab[2011DP173015] ; Youth Innovation Promotion Association, CAS[Y2021101]
WOS研究方向	Biochemistry & Molecular Biology ; Chemistry
WOS类目	Biochemistry & Molecular Biology ; Chemistry, Multidisciplinary
WOS记录号	WOS:000818191900001
出版者	MDPI
引用统计	被引频次：3[WOS] [WOS记录] [WOS相关记录]
文献类型	期刊论文
条目标识符	http://119.78.100.204/handle/2XEOYT63/19523
专题	中国科学院计算技术研究所期刊论文_英文
通讯作者	Peng, Yin; Wei, Yanjie
作者单位	1.Chinese Acad Sci, Shenzhen Inst Adv Technol, Joint Engn Res Ctr Hlth Big Data Intelligent Anal, Ctr High Performance Comp, Shenzhen 518055, Peoples R China 2.Univ Chinese Acad Sci, Sch Comp Sci & Technol, Beijing 100049, Peoples R China 3.Bangabandhu Sheikh Mujibur Rahaman Sci & Technol, Dept Stat, Gopalganj 8100, Bangladesh 4.Shenzhen Univ, Sch Med, Dept Pathol, Shenzhen 518060, Peoples R China
推荐引用方式 GB/T 7714	Hossain, Md. Tofazzal,Zhang, Jingjing,Reza, Md. Selim,et al. Reconstruction of Full-Length circRNA Sequences Using Chimeric Alignment Information[J]. INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES,2022,23(12):15.
APA	Hossain, Md. Tofazzal,Zhang, Jingjing,Reza, Md. Selim,Peng, Yin,Feng, Shengzhong,&Wei, Yanjie.(2022).Reconstruction of Full-Length circRNA Sequences Using Chimeric Alignment Information.INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES,23(12),15.
MLA	Hossain, Md. Tofazzal,et al."Reconstruction of Full-Length circRNA Sequences Using Chimeric Alignment Information".INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES 23.12(2022):15.