CPC: assess the protein-coding potential of transcripts using sequence   features and support vector machine

doi:10.1093/nar/gkm391

CORC > 北京大学 > 生命科学学院

	CPC: assess the protein-coding potential of transcripts using sequence features and support vector machine
	Kong, Lei ; Zhang, Yong ; Ye, Zhi-Qiang ; Liu, Xiao-Qiao ; Zhao, Shu-Qi ; Wei, Liping ; Gao, Ge
刊名	核酸研究
	2007
关键词	NONCODING RNA MAMMALIAN GENOME EXPRESSION DATA DATABASE PREDICTION EST
DOI	10.1093/nar/gkm391
英文摘要	Recent transcriptome studies have revealed that a large number of transcripts in mammals and other organisms do not encode proteins but function as noncoding RNAs (ncRNAs) instead. As millions of transcripts are generated by large-scale cDNA and EST sequencing projects every year, there is a need for automatic methods to distinguish protein-coding RNAs from noncoding RNAs accurately and quickly. We developed a support vector machine-based classifier, named Coding Potential Calculator (CPC), to assess the protein-coding potential of a transcript based on six biologically meaningful sequence features. Tenfold cross-validation on the training dataset and further testing on several large datasets showed that CPC can discriminate coding from noncoding transcripts with high accuracy. Furthermore, CPC also runs an order-of-magnitude faster than a previous state-of-the-art tool and has higher accuracy. We developed a user-friendly web-based interface of CPC at http://cpc.cbi.pku.edu.cn. In addition to predicting the coding potential of the input transcripts, the CPC web server also graphically displays detailed sequence features and additional annotations of the transcript that may facilitate users' further investigation.; http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=LinksAMR&KeyUT=WOS:000255311500065&DestLinkType=FullRecord&DestApp=ALL_WOS&UsrCustomerID=8e1609b174ce4e31116a60747a720701 ; Biochemistry & Molecular Biology; SCI(E); PubMed; 293; ARTICLE; Web Server issue; W345-W349; 35
语种	英语
内容类型	期刊论文
源URL	[http://ir.pku.edu.cn/handle/20.500.11897/320021]
专题	生命科学学院
推荐引用方式 GB/T 7714	Kong, Lei,Zhang, Yong,Ye, Zhi-Qiang,et al. CPC: assess the protein-coding potential of transcripts using sequence features and support vector machine[J]. 核酸研究,2007.
APA	Kong, Lei.,Zhang, Yong.,Ye, Zhi-Qiang.,Liu, Xiao-Qiao.,Zhao, Shu-Qi.,...&Gao, Ge.(2007).CPC: assess the protein-coding potential of transcripts using sequence features and support vector machine.核酸研究.
MLA	Kong, Lei,et al."CPC: assess the protein-coding potential of transcripts using sequence features and support vector machine".核酸研究 (2007).