Table 1.

Computational and experimental approaches to protein-coding sORFs.

Metrics and methods to identify sORF (including both computational and experimental)		Description	References
Computing-based method	sORFfinder, HAItORF, uPEPperoni	Web based tools to locate sORF having coding potential	Hanada et al., 2010; Vanderperre et al., 2012; Skarshewski et al., 2014
	PhyloCSF	A computational method examines evolutionary conservation of a sORF across species	Lin et al., 2011
Transcriptomic-based method	Ribosome profiling	A deep sequencing- based tool of ribosome protected mRNA fragments to obtain a global snapshot of translation	Ingolia et al., 2011
	Poly-ribo seq	A combination of ribosome profiling and polysome to enrich more potent protein coding ORFs	Aspden et al., 2014
	Ribosome releasing scores (RRS)	These three metrics are developed and combined with ribosome profiling to assist in identification of true protein coding ORFs	Guttman et al., 2013
	Fragment length organization similarity score (FLOSS)		Ingolia et al., 2014
	ORF regression algorithm for translation evaluation RPFS (ribosome-protected mRNA fragments) (ORF-RATER)		Fields et al., 2015
Proteomics-based	Proteo genomics	A combined approach of proteomics and genomics	Slavoff et al., 2013