Skip to main content

Table 1 Bioinformatics tools for identifying circRNA coding potential

From: Translation and functional roles of circular RNAs in human cancer

Algorithms Annotation Refs
ORF Finder This tool is to find all possible ORFs in the sequence provided by user [80]
CPC This tool is to assess the protein-coding potential of a transcript based on six biologically meaningful sequence features [81]
PhyloCSF This tool is to determine whether the sequence is likely to represent a conserved protein-coding region using multiple alignments to calculate the phylogenetic conservation score [82]
CPAT An alignment-free algorithm to distinguish between coding and noncoding transcripts on the basis of four sequence features [83]
IRESite A database that can be used to examine the cellular internal ribosome entry sites [80]
CircInteractome A database allow the investigation of potential circRNA translation through IRES sequences [84]
IRES finder An improved computation method which can be used to perform a comprehensive search of IRES [85]
Pfam A tool for the homology search of a putative product sequence [86]
NetNGlyc 1.0 A tool for N-Glycosylation sites prediction [87]
NetOGlyc 3.1 A tool for Mucin-type O-glycosylation sites prediction [87]
NetPhos 3.1 A tool for phosphorylation sites prediction [87]
CircPro An integrated tool for the identification of circRNAs with protein-coding potential [88]
CircCode An integrated tool for the identification of circRNAs with protein-coding potential [89]