Table 3.

Some bioinformatic resources for coding potential of sORF.

Tools	Data Requirement	Principle Utilized	URL	Ref.
CRITICA	Whole genome	Nucleotide sequence composition	http://rdpwww.life.uiuc.edu (The website link is temporarily unavailable)	[95]
CPC/CPC2	RNA-seq	Nucleotide composition, sequence similarity	http://cpc2.gao-lab.org/	[96]
PLEK	RNA-seq	Kmer composition of sequence	https://sourceforge.net/projects/plek	[97]
micPDP	RNA-seq	Codon conservation	https://github.com/Drmirdeep/micpdp.git	[98]
PhlyoCSF	RNA-seq	Codon substitution, nucleotide sequence similarity	http://compbio.mit.edu/PhyloCSF	[99]
PhastCons	Whole genome	Nucleotide composition	http://compgen.cshl.edu/phast/	[100]
sORF finder	Any nucleotide sequence	Nucleotide composition	http://evolver.psc.riken.jp/ (The website link is temporarily unavailable)	[101]
RNAcode	RNA-seq	Codon conservation	https://github.com/ViennaRNA/RNAcode.git	[102]
CNCI	RNA-seq	Nucleotide composition	https://github.com/www-bioinfo-org/CNCI.git	[103]
CPAT	RNA-seq	Permutation-free logistic regression model	https://wlcb.oit.uci.edu/cpat	[104]
CNIT	RNA-seq	Nucleotide composition	https://github.com/www-bioinfo-org/CNCI.git	[105]
ORF finder	Whole genome	Nucleotide composition	https://www.ncbi.nlm.nih.gov/orffinder/	[106]
iSeeRNA	RNA-seq	Machine-learning model	http://www.myogenesisdb.org/iSeeRNA (The website link is temporarily unavailable)	[107]
COME	RNA-seq	Machine-learning model	https://github.com/lulab/COME.git	[108]
LncRNA-ID	RNA-seq	Machine-learning model	https://github.com/zhangy72/LncRNA-ID.git	[109]
lncRNA-MFDL	RNA-seq	Deep-learning classification algorithms	http://compgenomics.utsa.edu/lncRNA_MDFL/	[110]
uPEPperoni	RNA-seq	Codon substitution	http://upep-scmb.biosci.uq.edu.au	[111]
DeepCPP	RNA-seq	Machine-learning algorithms	https://github.com/yuuuuzhang/DeepCPP.git	[112]
RNAsamba	RNA-seq	Similarity to known proteins	https://rnasamba.lge.ibi.unicamp.br/	[113]
MipepID	Whole genome	Machine-learning algorithms	https://github.com/MindAI/MiPepid.git	[114]