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] |