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

文献类型：期刊论文

作者Zhang, Jingjing6; Zhang, Huiling5; Ju, Zhen6; Peng, Yin; Pan, Yi3,4; Xi, Wenhui2; Wei, Yanjie1
刊名BRIEFINGS IN BIOINFORMATICS
出版日期2023-09-22
卷号24期号:6页码:11
关键词circRNA full-length sequence transcriptome junction contig
ISSN号1467-5463
DOI10.1093/bib/bbad363
英文摘要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.
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
语种英语
WOS记录号WOS:001136371500031
出版者OXFORD UNIV PRESS
源URL[http://119.78.100.204/handle/2XEOYT63/38419]  
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.Chinese Acad Sci, Shenzhen Inst Adv Technol, Ctr High Performance Comp, Shenzhen, Peoples R China
2.Chinese Acad Sci, Shenzhen Inst Adv Technol, Shenzhen, Peoples R China
3.Chinese Acad Sci, Shenzhen Inst Adv Technol, Coll Comp Sci & Control Engn, Shenzhen, Peoples R China
4.Shenzhen Univ, Dept Pathol, Shenzhen, Peoples R China
5.South China Agr Univ, Guangzhou, Peoples R China
6.Univ Chinese Acad Sci, Beijing, 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.

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来源：计算技术研究所

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