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. 2017 Jul 3;45(W1):W12-W16.
doi: 10.1093/nar/gkx428.

CPC2: a fast and accurate coding potential calculator based on sequence intrinsic features

Yu-Jian Kang  1 , De-Chang Yang  1 , Lei Kong  1 , Mei Hou  1 , Yu-Qi Meng  1 , Liping Wei  1 , Ge Gao  1
Affiliations

CPC2: a fast and accurate coding potential calculator based on sequence intrinsic features

Yu-Jian Kang et al. Nucleic Acids Res. .

Abstract

With advances in next-generation sequencing technologies, numerous novel transcripts in a large number of organisms have been identified. With the goal of fast, accurate assessment of the coding ability of RNA transcripts, we upgraded the coding potential calculator CPC1 to CPC2. CPC2 runs ∼1000 times faster than CPC1 and exhibits superior accuracy compared with CPC1, especially for long non-coding transcripts. Moreover, the model of CPC2 is species-neutral, making it feasible for ever-growing non-model organism transcriptomes. A mobile-friendly web server, as well as a downloadable standalone package, is freely available at http://cpc2.cbi.pku.edu.cn.

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Figures

Figure 1.
Figure 1.
Evaluation on accuracy of CPC1 and CPC2 in six species. (A) The overall accuracy (B) the detailed accuracy in six organisms. The Long ncRNAs were defined as non-coding RNAs longer than 200 nt.
Figure 2.
Figure 2.
Workflow of the CPC2 web server.
Figure 3.
Figure 3.
Screenshot of the CPC2 web server. (A) Summary tabular output with coding probability; (B) graphical view of features’ distribution in the ‘Details’ page; (C) more analysis for querying against known databases, re-analyzing in alternative methods and annotating functions; (D) the rendered BLAST output including both ORF position and BLAST hits in queried databases.
See this image and copyright information in PMC

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