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Table 1 Classification of prediction methods for ORFs

From: Emerging role of tumor-related functional peptides encoded by lncRNA and circRNA

Name Characteristics Website
CircRNADb [81] It includes 32,914 circRNA records for human exons. Each of them has IRES sequence components, predicted ORFs, related references, and so on. The predicted ORF is usually the cross-splicing site. http://202.195.183.4:8000/circrnadb/circRNADb.php
sORFs.org [82, 83] It comprises > 4,374,422 sORFs from six different species and derived from multiple ribosome profiling and sequencing datasets. http://www.sorfs.org
ORF Finder [84] It performs six-frame translations and returns the range of each ORF and its protein translation. These may be submitted directly for BLAST similarity or COGs database searches. https://www.ncbi.nlm.nih.gov/orffinder/
ORF Predictor [85] It was designed to predict expressed sequence tags (EST) or cDNA sequences. Its output file consists of predicted coding DNA sequences, the start and end of the coding region, and the protein peptide sequence. http://bioinformatics.ysu.edu/tools/OrfPredictor.html
SMS:ORF Finder [86] It searches for newly-sequenced DNA and returns the range of each ORF and its protein translation. SMS:ORF Finder supports the entire IUPAC alphabet and several genetic codes. http://www.bioinformatics.org/sms2/orf_find.html
CSCD [87] It contains cancer-associated circRNA alternative splicing, expression, and translation (ORF). It is linked to UCSC which predicts potential ORFs and highlight translatable circRNAs. http://gb.whu.edu.cn/CSCD/
PhyloCSF [88,89,90,91] It is based on the phylogenetic analysis of multi-species genomic sequence alignments and identifies conserved protein coding regions. It requires complete ORF sequences from different species to be able to evaluate their coding probabilities. http://compbio.mit.edu/PhyloCSF/
CircPro [92] Its data was derived from high-throughput sequencing (RNA-Seq and Ribo-Seq). It generates a list of circRNAs and reports genomic locations, ORF lengths, junction reads from Ribo-Seq, and so on. http://bis.zju.edu.cn/CircPro/
cORF_pipeline [93, 94] Its output predicts sORF sequences, start and stop positions, annotation data, and so on. The longest ORF spanning the circRNA splicing site is the one most likely to encode. https://github.com/kadenerlab/cORF_pipeline
CircBank [95] Its output contains the ORF size, the coding potential, and circRNA conservation. http://www.circbank.cn/index.html