TABLE 3.

Overview of the computational tools aiding in the prediction of sORFs.

Method	Features utilized	Input requirement	Output dataset	Reference and links
Sequence-based prediction tools
CPC2	Nucleotide composition, sequence similarity	RNA-seq	Coding potential of especially lncRNAs	(Kang et al., 2017) and GitHub
micPDP	Codon conservation	RNA-seq	sORF detection from non-coding RNA	Bazzini et al. (2014)
PhyloCSF	Codon substitution	RNA-seq	Coding potential	(Lin et al., 2011) and GitHub
PhastCons	Nucleotide composition	Whole genome	Conserved elements, especially signatures outside a protein-coding region	(Siepel et al., 2005; Crappé et al., 2013) and GitHub
sORF finder	Nucleotide composition similarity	Any nucleotide sequence	sORFs	(Hanada et al., 2010) and Link
Ribosome profiling-based tools
FLOSS	Ribosome fragment length	Ribo-seq	True ribosome footprints	Ingolia et al. (2014)
ORFscore	3-nt periodicity	Ribo-seq	Ribo-seq ORFs	Wu et al. (2020)
ORFquant	3-nt periodicity, transcript features such as exonic bins and splice junctions	Ribo-seq	Ribo-seq ORFs on multiple transcript isoforms	(Calviello et al., 2020) and GitHub
ORF-RATER	Read density over start and stop codons	Ribo-seq	Ribo-seq ORFs	(Fields et al., 2015) and GitHub
RiboTaper	3-nt periodicity	Ribo-seq, RNA-seq	Ribo-seq ORFs	(Calviello et al., 2016) and Link
RiboNT	3-nt periodicity (noise tolerant), codon usage	Ribo-seq	Ribo-seq ORFs	(Song et al., 2021) and GitHub
Ribotricer	3-nt periodicity	Ribo-seq	Ribo-seq ORFs, especially sORFs	(Choudhary et al., 2020) and GitHub
RRS	Read density drop after stop codon	Ribo-seq	Ribo-seq ORFs	Guttman et al. (2013)
SPECtre	3-nt periodicity	Ribo-seq	Ribo-seq ORFs	(Chun et al., 2016) and GitHub
TOC	Ribosome footprint patterns	Ribo-seq	Ribo-seq ORFs	Chew et al. (2013)
PROTEOFORMER	3-nt periodicity, Mass spec hits	Ribo-seq, Mass spec	Ribo-seq ORFs, MS ORFs	(Verbruggen et al., 2019) and GitHub