CircPro specifications

Information


Unique identifier OMICS_19663
Name CircPro
Software type Pipeline/Workflow
Interface Command line interface
Restrictions to use None
Input data Some genome reference file, gene annotation file, total RNA-Seq file, Ribo-Seq file and rRNA sequence file.
Output data An identified circRNA list.
Output format FASTA
Operating system Unix/Linux, Mac OS
Programming languages Perl
Computer skills Advanced
Stability Stable
Requirements
BWA, Bioperl, Bowtie, Samtools, NCBI BLAST, FASTX-Toolkit
Source code URL http://bis.zju.edu.cn/CircPro/CircPro.tar.gz
Maintained Yes

Versioning


No version available

Documentation


Maintainers


  • person_outline Ming Chen
  • person_outline Xianwen Meng

Publication for CircPro

CircPro citations

 (2)
library_books

Encoding activities of non coding RNAs

2018
Theranostics
PMCID: 5928905
PMID: 29721095
DOI: 10.7150/thno.24677

[…] the widespread N6-methyladenosine (m6A)-driven translation of circRNA, which was further proved by MS, computational prediction and polysome profiling . Meng et al. designed an integrated tool named CircPro to detect circRNAs with protein-coding potential . It was shown that a series of circRNAs was actually translated in a cap-independent manner . The produced small peptides or proteins have spe […]

library_books

Circular RNAs: Biogenesis, Function, and a Role as Possible Cancer Biomarkers

2017
Int J Genomics
PMCID: 5733622
PMID: 29349062
DOI: 10.1155/2017/6218353

[…] S, CIRI, MapSplice, and segemehl utilize the fragmented-based approach. In addition, several integrated tools aimed to identify circRNAs with a protein-coding potential have been developed, including CircPro [], IRESite [], CPAT [], Pfam 31.0 [], PhyloCSF [], and ORF Finder from the NCBI database. Also, the TopHat-Fusion algorithm has been designed to detect circRNAs that are derived from gene fus […]

CircPro institution(s)
Department of Bioinformatics, State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, China
CircPro funding source(s)
Supported by the National Natural Science Foundation of China (Nos: 31371328, 31450110068 and 31571366); National Key Research and Development Program of China (No.2016YFA0501704); Science Technology Department of Zhejiang Province (No.2015C32057); the Fundamental Research Funds for the Central Universities; Jiangsu Collaborative Innovation Center for Modern Crop Production and the Program for Innovative Research Team in Zhejiang University.

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