Table 1 sORF prediction tools

Coding Non-Coding Identifying Tool (CNIT)

[126]

http://cnit.noncode.org/CNIT/

Distinguishes between coding and non-coding regions based on intrinsic sequence compositions

Coding Region Identification Tool Invoking Comparative Analysis (CRITICA)

[127]

http://rdpwww.life.uiuc.edu/

Analyses nucleotide sequence composition and conservation at the amino acid level

Coding Potential Calculator (CPC)/CPC2

[128, 129]

http://cpc.cbi.pku.edu.cn

http://cpc2.gao-lab.org/

Assess protein-coding potential based on important features (ORF size, coverage, integrity); CPC2 improves run speed and accuracy

Coding Potential Predictor (CPPred)

[130]

http://www.rnabinding.com/CPPred/

Predicts the coding potential of RNA transcript

CPPred-sORF

[131]

http://www.rnabinding.com/CPPred-sORF/

Addition of 2 new features from CCPred i.e., GCcount, mRNN-11codons and CUG, GUG start codons

MicroPeptide Tool (MiPepid)

[21]

https://github.com/MindAI/MiPepid

Identifies coding sORFs based on existing microproteins subpopulation set

sORF Finder

[52]

http://evolver.psc.riken.jp/

Identifies sORF with high coding potential based on nucleotide composition bias and potential functional constraint at the amino acid level

smORFunction

[132]

https://www.cuilab.cn/smorfunction/home

Provides function prediction of sORFs/microproteins

miPFinder

[133]

https://github.com/DaStraub/miPFinder

Identifies and evaluates microproteins functionality using information on size, domain, protein interactions and evolutionary origin

PhastCons

[134]

http://compgen.cshl.edu/phast/

Based on conservation scoring and identification of conserved elements

PhyloCSF

[135]

http://compbio.mit.edu/PhyloCSF

Determines a conserved protein-coding region based on formal statistical comparison of phylogenetic codon models

uPEPperoni

[136]

http://upep-scmb.biosci.uq.edu.au/

Specifically for 5’UTR sORFs, based on conservation

AnABLAST

[34]

http://www.bioinfocabd.upo.es/ab/

Identifies putative protein-coding regions in DNA regardless of ORF length and reading frame shifts

Small Peptide Alignment Discovery Application (SPADA)

[137]

https://github.com/orionzhou/SPADA

Homology-based gene prediction programme

Deep Neural Network for coding potential prediction (DeepCPP)

[138]

https://github.com/yuuuuzhang/DeepCPP

Effective on RNA coding potential prediction, spefically sORF mRNA prediction