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

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

doi:10.1093/nar/gkx428

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

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

Authors

Yu-Jian Kang¹, De-Chang Yang¹, Lei Kong¹, Mei Hou¹, Yu-Qi Meng¹, Liping Wei¹, Ge Gao¹

Affiliation

¹ State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Center for Bioinformatics, Peking University, Beijing 100871, People's Republic of China.

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.

Publication types

Evaluation Study
Research Support, Non-U.S. Gov't

MeSH terms

Algorithms
Animals
Gene Expression Profiling
High-Throughput Nucleotide Sequencing / methods*
Humans
Internet
Mice
RNA, Long Noncoding / chemistry
RNA, Messenger / chemistry
RNA, Small Untranslated / chemistry
Sequence Analysis, RNA / methods*
Software*

Substances

RNA, Long Noncoding
RNA, Messenger
RNA, Small Untranslated