FcircSEC: An R Package for Full Length circRNA Sequence Extraction and Classification

doi:10.1155/2020/9084901

	FcircSEC: An R Package for Full Length circRNA Sequence Extraction and Classification
	Hossain, Md. Tofazzal 1,2; Peng, Yin 3; Feng, Shengzhong 1; Wei, Yanjie 1
	2020-06-01
发表期刊	INTERNATIONAL JOURNAL OF GENOMICS
ISSN	2314-436X
卷号	2020 页码:11
摘要	Circular RNAs (circRNAs) are formed by joining the 3 ' and 5 ' ends of RNA molecules. Identification of circRNAs is an important part of circRNA research. The circRNA prediction methods can predict the circRNAs with start and end positions in the chromosome but cannot identify the full-length circRNA sequences. We present an R package FcircSEC (Full Length circRNA Sequence Extraction and Classification) to extract the full-length circRNA sequences based on gene annotation and the output of any circRNA prediction tools whose output has a chromosome, start and end positions, and a strand for each circRNA. To validate FcircSEC, we have used three databases, circbase, circRNAdb, and plantcircbase. With information such as the chromosome and strand of each circRNA as the input, the identified sequences by FcircSEC are consistent with the databases. The novelty of FcircSEC is that it can take the output of state-of-the-art circRNA prediction tools as input and is applicable for human and other species. We also classify the circRNAs as exonic, intronic, and others. The R package FcircSEC is freely available.
DOI	10.1155/2020/9084901
收录类别	SCI
语种	英语
资助项目	National Key Research and Development Program of China[2018YFB0204403] ; National Key Research and Development Program of China[2016YFB0201305] ; National Science Foundation of China[U1813203] ; National Science Foundation of China[61433012] ; Shenzhen Basic Research Fund[JCYJ20180507182818013] ; Shenzhen Basic Research Fund[JCYJ20170413093358429] ; China Postdoctoral Science Foundation[2019M653132] ; CAS Key Lab[2011DP173015] ; Shenzhen Discipline Construction Project for Urban Computing and Data Intelligence, Youth Innovation Promotion Association, CAS
WOS研究方向	Biochemistry & Molecular Biology ; Biotechnology & Applied Microbiology ; Genetics & Heredity
WOS类目	Biochemistry & Molecular Biology ; Biotechnology & Applied Microbiology ; Genetics & Heredity
WOS记录号	WOS:000542668200003
出版者	HINDAWI LTD
引用统计	被引频次：10[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/2XEOYT63/15168
专题	中国科学院计算技术研究所期刊论文_英文
通讯作者	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, Guangdong, Peoples R China 2.Univ Chinese Acad Sci, 19 A Yuquan Rd, Beijing 100049, Peoples R China 3.Shenzhen Univ, Sch Med, Dept Pathol, Shenzhen 518060, Guangdong, Peoples R China
推荐引用方式 GB/T 7714	Hossain, Md. Tofazzal,Peng, Yin,Feng, Shengzhong,et al. FcircSEC: An R Package for Full Length circRNA Sequence Extraction and Classification[J]. INTERNATIONAL JOURNAL OF GENOMICS,2020,2020:11.
APA	Hossain, Md. Tofazzal,Peng, Yin,Feng, Shengzhong,&Wei, Yanjie.(2020).FcircSEC: An R Package for Full Length circRNA Sequence Extraction and Classification.INTERNATIONAL JOURNAL OF GENOMICS,2020,11.
MLA	Hossain, Md. Tofazzal,et al."FcircSEC: An R Package for Full Length circRNA Sequence Extraction and Classification".INTERNATIONAL JOURNAL OF GENOMICS 2020(2020):11.