CPAT pipeline

CPAT specifications

Information


Unique identifier OMICS_05862
Name CPAT
Alternative name Coding Potential Assessment Tool
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input format BED, FASTA
Operating system Unix/Linux
Programming languages C, Python
License GNU General Public License version 2.0
Computer skills Advanced
Stability Stable
Maintained Yes

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Maintainer


  • person_outline Wei Li <>

Information


Unique identifier OMICS_05862
Name CPAT
Alternative name Coding Potential Assessment Tool
Interface Web user interface
Restrictions to use None
Input format BED, FASTA
Programming languages C, Python
Computer skills Basic
Stability Stable
Maintained Yes

Maintainer


  • person_outline Wei Li <>

Publication for Coding Potential Assessment Tool

CPAT IN pipelines

 (6)
2017
PMCID: 5356381
PMID: 28272462
DOI: 10.1038/srep44033

[…] with known transcripts or were within 1000 bp of the nearest coding genes. finally, to obtain reliable novel lincrnas, the coding potential of putative lincrnas were calculated using cpc48 and cpat49, two robust approaches for distinguishing coding from noncoding rnas. only those transcripts with a cpc score <0 and a cpat score <0.364 were retained as novel putative lincrnas […]

2017
PMCID: 5356381
PMID: 28272462
DOI: 10.1038/srep44033

[…] coding potential of putative lincrnas were calculated using cpc48 and cpat49, two robust approaches for distinguishing coding from noncoding rnas. only those transcripts with a cpc score <0 and a cpat score <0.364 were retained as novel putative lincrnas for the analysis., the r package “edger”50 was used to identify differentially expressed transcripts between tumor and adjacent normal […]

2017
PMCID: 5548780
PMID: 28790305
DOI: 10.1038/s41467-017-00319-8

[…] default parameters. all of the predicted assemblies from all nuclei were merged using cuffmerge version 2.1.1. the predicted transcripts in the merged assembly were checked for coding potential with cpat37. cpat uses a logistic regression model built with four sequence features for protein-coding potential prediction, including open reading frame size, open reading frame coverage, fickett […]

2017
PMCID: 5548780
PMID: 28790305
DOI: 10.1038/s41467-017-00319-8

[…] parameters. all of the predicted assemblies from all nuclei were merged using cuffmerge version 2.1.1. the predicted transcripts in the merged assembly were checked for coding potential with cpat37. cpat uses a logistic regression model built with four sequence features for protein-coding potential prediction, including open reading frame size, open reading frame coverage, fickett testcode […]

2017
PMCID: 5548780
PMID: 28790305
DOI: 10.1038/s41467-017-00319-8

[…] model built with four sequence features for protein-coding potential prediction, including open reading frame size, open reading frame coverage, fickett testcode statistic, and hexamer usage bias. cpat reports the protein-coding probability score in the range between 0 and 1, but the optimum probability cutoff varies with different organism. for mouse, we used optimum cutoff determined […]

CPAT institution(s)
Division of Biomedical Statistics and Informatics, Mayo Clinic College of Medicine, Chinahester, MN, USA; Division of Biostatistics, Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, TX, USA; Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA; State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, Jiangsu, China

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