JCcirc: circRNA full-length sequence assembly through integrated junction contigs

doi:10.1093/bib/bbad363

	JCcirc: circRNA full-length sequence assembly through integrated junction contigs
	Zhang, Jingjing 1; Zhang, Huiling 2; Ju, Zhen 1; Peng, Yin ; Pan, Yi 3,4; Xi, Wenhui 5; Wei, Yanjie 6
	2023-09-22
发表期刊	BRIEFINGS IN BIOINFORMATICS
ISSN	1467-5463
卷号	24 期号:6 页码:11
摘要	Recent studies have shed light on the potential of circular RNA (circRNA) as a biomarker for disease diagnosis and as a nucleic acid vaccine. The exploration of these functionalities requires correct circRNA full-length sequences; however, existing assembly tools can only correctly assemble some circRNAs, and their performance can be further improved. Here, we introduce a novel feature known as the junction contig (JC), which is an extension of the back-splice junction (BSJ). Leveraging the strengths of both BSJ and JC, we present a novel method called JCcirc (https://github.com/cbbzhang/JCcirc). It enables efficient reconstruction of all types of circRNA full-length sequences and their alternative isoforms using splice graphs and fragment coverage. Our findings demonstrate the superiority of JCcirc over existing methods on human simulation datasets, and its average F1 score surpasses CircAST by 0.40 and outperforms both CIRI-full and circRNAfull by 0.13. For circRNAs below 400 bp, 400-800 bp, 800 bp-1200 bp and above 1200 bp, the correct assembly rates are 0.13, 0.09, 0.04 and 0.03 higher, respectively, than those achieved by existing methods. Moreover, JCcirc also outperforms existing assembly tools on other five model species datasets and real sequencing datasets. These results show that JCcirc is a robust tool for accurately assembling circRNA full-length sequences, laying the foundation for the functional analysis of circRNAs.
关键词	circRNA full-length sequence transcriptome junction contig
DOI	10.1093/bib/bbad363
收录类别	SCI
语种	英语
资助项目	Youth Innovation Promotion Association[Y2021101] ; Key Research and Development Project of Guangdong Province[2021B0101310002] ; National Key Research and Development Program of China[2021YFF1200100] ; Strategic Priority CAS Project[XDB38050100] ; National Science Foundation of China[62272449] ; Shenzhen Basic Research Fund[RCYX2020071411 4734194] ; Shenzhen Basic Research Fund[KQTD20200820113106007] ; Shenzhen Basic Research Fund[ZDSYS2022042210380 0001]
WOS研究方向	Biochemistry & Molecular Biology ; Mathematical & Computational Biology
WOS类目	Biochemical Research Methods ; Mathematical & Computational Biology
WOS记录号	WOS:001136371500031
出版者	OXFORD UNIV PRESS
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/2XEOYT63/38420
专题	中国科学院计算技术研究所期刊论文_英文
通讯作者	Xi, Wenhui; Wei, Yanjie
作者单位	1.Univ Chinese Acad Sci, Beijing, Peoples R China 2.South China Agr Univ, Guangzhou, Peoples R China 3.Shenzhen Univ, Dept Pathol, Shenzhen, Peoples R China 4.Chinese Acad Sci, Shenzhen Inst Adv Technol, Coll Comp Sci & Control Engn, Shenzhen, Peoples R China 5.Chinese Acad Sci, Shenzhen Inst Adv Technol, Shenzhen, Peoples R China 6.Chinese Acad Sci, Shenzhen Inst Adv Technol, Ctr High Performance Comp, Shenzhen, Peoples R China
推荐引用方式 GB/T 7714	Zhang, Jingjing,Zhang, Huiling,Ju, Zhen,et al. JCcirc: circRNA full-length sequence assembly through integrated junction contigs[J]. BRIEFINGS IN BIOINFORMATICS,2023,24(6):11.
APA	Zhang, Jingjing.,Zhang, Huiling.,Ju, Zhen.,Peng, Yin.,Pan, Yi.,...&Wei, Yanjie.(2023).JCcirc: circRNA full-length sequence assembly through integrated junction contigs.BRIEFINGS IN BIOINFORMATICS,24(6),11.
MLA	Zhang, Jingjing,et al."JCcirc: circRNA full-length sequence assembly through integrated junction contigs".BRIEFINGS IN BIOINFORMATICS 24.6(2023):11.