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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

Download


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Versioning


No version available

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

 (200)
library_books

Genome wide analysis of differentially expressed profiles of mRNAs, lncRNAs and circRNAs during Cryptosporidium baileyi infection

2018
BMC Genomics
PMCID: 5946474
PMID: 29747577
DOI: 10.1186/s12864-018-4754-2

[…] Four analytic tools, namely coding-non-coding-index (CNCI) [], coding potential calculator (CPC) [], phylogenetic codon substitution frequency (PhyloCSF) [] and Pfam-scan [], were used to effectively distinguish protein-coding and non-coding sequences. Ultimately […]

library_books

Whole transcriptome analysis of atrophic ovaries in broody chickens reveals regulatory pathways associated with proliferation and apoptosis

2018
Sci Rep
PMCID: 5940789
PMID: 29739971
DOI: 10.1038/s41598-018-25103-6

[…] .3.12). The reconstruction and identification of transcripts was carried out with the software Cufflinks, TopHat2, Cuffmerge, and Cuffcompare. The programs Coding-Non-Coding-Index (CNCI) (version 2), Coding Potential Calculator (CPC) (http://cpc.cbi.pku.edu.cn/) and phylogenetic codon substitution frequency (PhyloCSF) were used to predict the protein-coding potential of new transcripts with defaul […]

library_books

Genome wide differential expression profiling of mRNAs and lncRNAs associated with prolificacy in Hu sheep

2018
Biosci Rep
PMCID: 5920141
PMID: 29439142
DOI: 10.1042/BSR20171350

[…] sembled transcripts were annotated using the Cuffcompare program from the Cufflinks package. Unknown transcripts were used to screen for putative lncRNAs. Four computational approaches, including the coding potential calculator (cpc), coding-non-coding index (cnci), protein families database (pfam), and coding-potential assessment tool (cpat) [], were combined to sort non-protein-coding RNA candid […]

library_books

Characterization of lncRNAs involved in cold acclimation of zebrafish ZF4 cells

2018
PLoS One
PMCID: 5892903
PMID: 29634734
DOI: 10.1371/journal.pone.0195468

[…] pts with known lncRNAs in the NONCODE2016 database and filter out the same or similar transcripts []. The remaining unknown transcripts were filtered by length 200 nt, exon number 1, ORF 300 nt. CPC (Coding Potential Calculator), CNCI (Coding Non-Coding Index) and Pfam were used to delete transcripts with coding potential [–]. Finally, we calculated fragments per kilobase per million mapped reads […]

library_books

Transcriptomic analysis reveals vacuolar Na+ (K+)/H+ antiporter gene contributing to growth, development, and defense in switchgrass (Panicum virgatum L.)

2018
BMC Plant Biol
PMCID: 5892015
PMID: 29631566
DOI: 10.1186/s12870-018-1278-5

[…] The assembled transcripts were compared with the annotated genomic transcripts from the reference sequences to identify novel transcribed regions. The coding potential calculator (CPC: http://cpc.cbi.pku.edu.cn/) was used to assess the protein-coding potential []. […]

library_books

A Key Gene, PLIN1, Can Affect Porcine Intramuscular Fat Content Based on Transcriptome Analysis

2018
Genes
PMCID: 5924536
PMID: 29617344
DOI: 10.3390/genes9040194

[…] pts were reconstructed using StringTie [], then reconstructed transcripts were compared to the reference annotation using Cuffcompare []. Coding potential of novel transcripts was predicted using the Coding Potential Calculator (CPC) []. Then, coded novel transcripts were merged with reference transcripts to obtain a complete reference, and downstream analysis was based on this reference. […]

Citations

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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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