Evaluation of CircRNA Sequence Assembly Methods Using Long Reads

doi:10.3389/fgene.2022.816825

	Evaluation of CircRNA Sequence Assembly Methods Using Long Reads
	Zhang, Jingjing 1,2; Hossain, Md. Tofazzal 1,2; Liu, Weiguo 3; Peng, Yin 4; Pan, Yi 2; Wei, Yanjie 2,5
	2022-02-14
发表期刊	FRONTIERS IN GENETICS
卷号	13 页码:12
摘要	The functional study on circRNAs has been increasing in the past decade due to its important roles in micro RNA sponge, protein coding, the initiation, and progression of diseases. The study of circRNA functions depends on the full-length sequences of circRNA, and current sequence assembly methods based on short reads face challenges due to the existence of linear transcript. Long reads produced by long-read sequencing techniques such as Nanopore technology can cover full-length sequences of circRNA and therefore can be used to evaluate the correctness and completeness of circRNA full sequences assembled from short reads of the same sample. Using long reads of the same samples, one from human and the other from mouse, we have comprehensively evaluated the performance of several well-known circRNA sequence assembly algorithms based on short reads, including circseq_cup, CIRI_full, and CircAST. Based on the F1 score, the performance of CIRI-full was better in human datasets, whereas in mouse datasets CircAST was better. In general, each algorithm was developed to handle special situations or circumstances. Our results indicated that no single assembly algorithm generated better performance in all cases. Therefore, these assembly algorithms should be used together for reliable full-length circRNA sequence reconstruction. After analyzing the results, we have introduced a screening protocol that selects out exonic circRNAs with full-length sequences consisting of all exons between back splice sites as the final result. After screening, CIRI-full showed better performance for both human and mouse datasets. The average F1 score of CIRI-full over four circRNA identification algorithms increased from 0.4788 to 0.5069 in human datasets, and it increased from 0.2995 to 0.4223 in mouse datasets.
关键词	circRNA full-length sequences short reads long reads assembly
DOI	10.3389/fgene.2022.816825
收录类别	SCI
语种	英语
资助项目	National Key Research and Development Program of China[2018YFB0204403] ; Strategic Priority CAS Project[XDB38050100] ; National Science Foundation of China[U1813203] ; National Natural Youth Science Foundation of China[31601028] ; Shenzhen Basic Research Fund[JCYJ20190808163801777] ; Shenzhen Basic Research Fund[KQTD20200820113106007] ; Shenzhen Basic Research Fund[RCYX2020071411473419] ; CAS Key Lab[2011DP173015]
WOS研究方向	Genetics & Heredity
WOS类目	Genetics & Heredity
WOS记录号	WOS:000761677600001
出版者	FRONTIERS MEDIA SA
引用统计	被引频次：4[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/2XEOYT63/18979
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.Univ Chinese Acad Sci, Beijing, Peoples R China 2.Chinese Acad Sci, Shenzhen Inst Adv Technol, Ctr High Performance Comp, Shenzhen, Peoples R China 3.Shandong Univ, Sch Software, Jinan, Peoples R China 4.Shenzhen Univ, Sch Med, Dept Pathol, Guangdong Key Lab Genome Stabil & Dis Prevent &, Shenzhen, Peoples R China 5.Chinese Acad Sci, Shenzhen Inst Adv Technol, CAS Key Lab Hlth Informat, Shenzhen, Peoples R China
推荐引用方式 GB/T 7714	Zhang, Jingjing,Hossain, Md. Tofazzal,Liu, Weiguo,et al. Evaluation of CircRNA Sequence Assembly Methods Using Long Reads[J]. FRONTIERS IN GENETICS,2022,13:12.
APA	Zhang, Jingjing,Hossain, Md. Tofazzal,Liu, Weiguo,Peng, Yin,Pan, Yi,&Wei, Yanjie.(2022).Evaluation of CircRNA Sequence Assembly Methods Using Long Reads.FRONTIERS IN GENETICS,13,12.
MLA	Zhang, Jingjing,et al."Evaluation of CircRNA Sequence Assembly Methods Using Long Reads".FRONTIERS IN GENETICS 13(2022):12.