Table 2.

Select sORF and SEP databases and resources^a

Primary use	Resource	ORF/SEP supporting evidence	Notable features	URL	Refs
Visualization	GWIPS-Viz	Ribo-Seq, Ti-Seq and RNA-Seq visualization from individual experiments and global aggregates	Online genome browser for visualizing processed Ribo-Seq data	https://gwips.ucc.ie/	[59]
	Trips-Viz	Ribo-Seq and MS data from individual experiments	Online browser for visualizing processed Ribo-Seq data. Can plot single nucleotide read intensity and predict translated ORFs	https://trips.ucc.ie/	[60]
Transcriptome-wide ORF predictions	RPFdb v2.0	Ribo-Seq	Comprehensive collection of Ribo-Seq studies with ORF predictions in a searchable browser	http://sysbio.gzzoc.com/rpfdb/index.html	[61]
	sORFs.org	Conservation Ribo-Seq MS	Incorporates multiple sORF scoring metrics and annotates sORFs with dozens of attributes	http://www.sorfs.org/	[62]
	Metamorf	Conservation Coding potential Kozak context Ribo-Seq MS	Includes UCSC genome browser session for visualization and introduces an ORF nomenclature	https://metamorf.hb.univ-amu.fr/	[63]
	smProt	Literature mining Database mining Ribo-Seq MS	Includes variant and disease specific annotations and maintains a high-confidence set	http://bigdata.ibp.ac.cn/SmProt/	[64]
	OpenProt	Ribo-Seq MS	Generates ORFeome by 3-frame transcriptome translation, then checks for evidence of translation	https://www.openprot.org/	[65]
	nORFs.org	sORFs.org openProt.org	Aggregates information from other databases and presents a fast, user-friendly interface, including a built-in genome browser	https://norfs.org/home	[66]
ORFs in noncoding RNA	LncPEP	Coding potential Conserved protein domains Ti-Seq Ribo-Seq m6A RNA modification	Focuses on lncRNAs. Determines a coding score based on a normalized sum of six input variables	http://www.shenglilabs.com/LncPep/	[67]
	SPENCER	MS	SEPs from ncRNA in cancer including predictions of MHC I affinity, stability, and TCR recognition probability	http://spencer.renlab.org/#/home	[68]
	Coding and noncoding RNA database	Literature review	Curated RNAs that have coding and noncoding functions with links to literature and supporting data	http://www.rna-society.org/cncrnadb/	[69]
Ribo-Seq web application	RiboToolkit	Predictions from uploaded FASTQs	Webserver that accepts Ribo-Seq FASTQs for analysis and implements a full prediction pipeline	http://rnabioinfor.tch.harvard.edu/RiboToolkit/	[41]

^aThese resources enable investigators to circumvent the technical and computational challenges of sORF prediction and move directly to the hypothesis-driven characterization phase. Indeed, given the thousands of predicted but unstudied sORFs, the greater benefit to the scientific community collectively might come from investigations of current predictions rather than new exploratory experiments.