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

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 tim...

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Detalles Bibliográficos
Autores principales: Kang, Yu-Jian, Yang, De-Chang, Kong, Lei, Hou, Mei, Meng, Yu-Qi, Wei, Liping, Gao, Ge
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2017
Materias:
Web Server Issue
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5793834/
https://www.ncbi.nlm.nih.gov/pubmed/28521017
http://dx.doi.org/10.1093/nar/gkx428
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author Kang, Yu-Jian
Yang, De-Chang
Kong, Lei
Hou, Mei
Meng, Yu-Qi
Wei, Liping
Gao, Ge
author_facet Kang, Yu-Jian
Yang, De-Chang
Kong, Lei
Hou, Mei
Meng, Yu-Qi
Wei, Liping
Gao, Ge
author_sort Kang, Yu-Jian
collection PubMed
description 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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spelling pubmed-57938342018-02-06 CPC2: a fast and accurate coding potential calculator based on sequence intrinsic features Kang, Yu-Jian Yang, De-Chang Kong, Lei Hou, Mei Meng, Yu-Qi Wei, Liping Gao, Ge Nucleic Acids Res Web Server Issue 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. Oxford University Press 2017-07-03 2017-05-18 /pmc/articles/PMC5793834/ /pubmed/28521017 http://dx.doi.org/10.1093/nar/gkx428 Text en © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research. http://creativecommons.org/licenses/by-nc/4.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com
spellingShingle Web Server Issue
Kang, Yu-Jian
Yang, De-Chang
Kong, Lei
Hou, Mei
Meng, Yu-Qi
Wei, Liping
Gao, Ge
CPC2: a fast and accurate coding potential calculator based on sequence intrinsic features
title CPC2: a fast and accurate coding potential calculator based on sequence intrinsic features
title_full CPC2: a fast and accurate coding potential calculator based on sequence intrinsic features
title_fullStr CPC2: a fast and accurate coding potential calculator based on sequence intrinsic features
title_full_unstemmed CPC2: a fast and accurate coding potential calculator based on sequence intrinsic features
title_short CPC2: a fast and accurate coding potential calculator based on sequence intrinsic features
title_sort cpc2: a fast and accurate coding potential calculator based on sequence intrinsic features
topic Web Server Issue
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5793834/
https://www.ncbi.nlm.nih.gov/pubmed/28521017
http://dx.doi.org/10.1093/nar/gkx428
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