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. Author manuscript; available in PMC: 2022 Jul 20.
Published in final edited form as: Wiley Interdiscip Rev RNA. 2021 Aug 2;13(1):e1685. doi: 10.1002/wrna.1685

Table 2. List of software or web tools required for identification of protein-coding circRNAs.

Tools Description Link References
RPFdb v2.0 An open-source repository of ribosome profiling data sets http://sysbio.gzzoc.com/rpfdb/ H. Wang et al. (2019)
CircPro A tool to identify protein-coding circRNAs using Ribo-Seq data http://bis.zju.edu.cn/CircPro/ Meng et al. (2017)
CircCode An advanced command-line-based tool to identify the coding circRNAs https://github.com/PSSUN/CircCode Sun & Li (2019)
Rcirc R package for detecting circRNAs and their coding potential https://github.com/PSSUN/Rcirc Sun et al. (2020)
ORF Finder Finds all possible ORFs in a given sequence https://www.ncbi.nlm.nih.gov/orffinder/
CPC2 Determine the protein-coding potential of a given transcript http://cpc2.cbi.pku.edu.cn Kang et al. (2017)
CPAT An align-free algorithm to analyze the coding potential of a given sequence http://code.google.com/p/cpat/ L. Wang et al. (2013)
PhyloCSF Identify conserved protein-coding sequences http://compbio.mit.edu/PhyloCSF Lin et al. (2011)
TISdb Database of TIS positions and ORFs based on GTI-seq data http://tisdb.human.cornell.edu/ Wan and Qian (2014)
preTIS Identify non-canonical translation initiation sites in the 5' UTR http://service.bioinformatik.uni-saarland.de/pretis Reuter et al. (2016)
TITER Identify all ORFs with AUG as well as non-AUG start codons https://github.com/zhangsaithu/titer S. Zhang et al. (2017)
IRESite Database of experimentally validated viral and cellular IRES regions http://www.iresite.org Mokrejs et al. (2010)
IRESbase Database of experimentally verified IRES elements http://reprod.njmu.edu.cn/cgi-bin/iresbase/index.php Zhao et al. (2020)
REPIC A database of N6-methyladenosine modifications https://repicmod.uchicago.edu/repic/ S. Liu et al. (2020)
circAtlas Database of circRNAs with IRES and ORF information http://circatlas.biols.ac.cn/ W. Wu et al. (2020)
circBank Database of human circRNAs m6A and proteincoding potential information http://www.circbank.cn/ M. Liu et al. (2019)
circRNADb Database of human circRNAs that includes information about translatable circRNAs http://reprod.njmu.edu.cn/circrnadb X. Chen et al. (2016)
TransCirc A database of human circRNAs with protein-coding potential https://www.biosino.org/transcirc/ W. Huang et al. (2021)
riboCirc Database of translatable circRNAs and their encoded proteins http://www.ribocirc.com/index.html H. Li et al. (2021)