CPC pipeline

CPC specifications

Information


Unique identifier OMICS_05864
Name CPC
Alternative names Coding Potential Calculator, CPC2
Interface Web user interface
Restrictions to use None
Input data RNA transcript sequences.
Input format FASTA, BED, GTF
Output data Html view, raw data, and results details consisting of a summary paragraph, a graphical view of detail information in feature distribution of your sequence and more information of additional evidences for coding potential.
Programming languages Java
License GNU General Public License version 3.0
Computer skills Basic
Version 2
Stability Beta
Maintained Yes

Maintainers


  • person_outline Liping Wei <>
  • person_outline Ge Gao <>
  • person_outline CPC Team <>

Additional information


http://cpc2.cbi.pku.edu.cn/help.php

Information


Unique identifier OMICS_05864
Name CPC
Alternative names Coding Potential Calculator, CPC2
Software type Application/Script
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages Python
License GNU General Public License version 3.0
Computer skills Advanced
Version 2
Stability Stable
Requirements Biopython package
Maintained Yes

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Maintainers


  • person_outline Liping Wei <>
  • person_outline Ge Gao <>
  • person_outline CPC Team <>

Additional information


http://cpc2.cbi.pku.edu.cn/help.php

Publications for Coding Potential Calculator

CPC citations

 (3)
2017
PMCID: 5344371

[…] were more likely to encode proteins, a python script was developed to ensure that transcripts that encoded orfs of 100 or less amino acids were considered as long non-coding rna candidates., the coding potential calculator (cpc) [29], which is based on the detection of quality, completeness, and sequence similarity of the orf to proteins in current protein databases, was utilized to detect […]

2017
PMCID: 5665958

[…] at least 500 bp away from neighbouring protein-coding or house-keeping genes are classified as intergenic transcripts, (4) the coding potential of intergenic transcripts was assessed using the coding potential calculator (cpc)56, and only those transcripts with a cpc score of less than −1 were defined as noncoding genes., reads from the study with the sra accession number of srp03798628 […]

2015
PMCID: 4366165

[…] tags database (dbest, ncbi, release 130101) [41] using the blastn algorithm (v2.2.26+, e-value threshold = 1e-5) [42]., all unknown transcripts were then evaluated for coding potential using the coding potential calculator (cpc) [43]. the cpc tool uses support vector machines to calculate the coding potential of a transcript. it takes e.g. open reading frame (orf) length, sequence […]

CPC institution(s)
State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Center for Bioinformatics, Peking University, Beijing, China
CPC funding source(s)
Supported by National Key Research and Development Program [2016YFC0901603], China 863 Program [2015AA020108], State Key Laboratory of Protein and Plant Gene Research and National Program for Support of Top-notch Young Professionals (in part).

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