Table 1.
Bioinformatic tools
| Methods based on sequence prediction | Reference | |
|---|---|---|
| PhyloCSF | Codon substitution and conservation elements | Sandmann et al., 202335 |
| OpenProt | Uses public available datasets to asses Ribo-seq and MS | Brunet et al., 201940 |
| RNASamba | Neuroal network to predict sORFs, recognizes Kozak sequence | Hanada et al., 201043 |
| DeepCPP | Algorithm using nucleotide bias to predict sORFs | Olexiouk et al., 201645 |
| MiPepid | Machine learning tool using for identificaton of sORFs based on known sORFs | Zhang et al., 202147 |
| csORF-finder | Uses trinucleotide deviation from expected mean to distinguish between coding sORFs from non-coding sORFs | Zhu and Gribskov, 201948 |
| ORFanage | Pseudo alignment algorithm for the detection of sORFs from RNA-seq data | Zhang et al., 202249 |
| sORF finder | Detection of sORFs according to 3-nucleotide composition bias | Brunet et al., 202142 |
| micPDP | Search for sORFs based on codon substitutions observed in whole-genome alignments | Bazzini et al., 20144 |
| uPEPperoni | Detection of uORFs based on location and transcript conservation | Skarshewski et al., 201444 |
| sORFs.org | Database of sORFs based on Ribo-seq data and integrates MS evidence and conservation searches | Li et al., 202146 |
| SmPROT | sORFs reported in literature, databases, Ribo-seq and MS data | Zhang et al., 202147 |
| Methods based on ribosome profiling | ||
| ORF-Rater | ORF Regression algorithm using Ribo-seq data to quantify translation regardless of start codon, overlap and length | Kute, et al., 202239 |
| ORFscore | Codon in-frame reads | Bazzini et al., 20144 |
| ORFquant | Annotation and quantification of tranlation level of ORFs considering multiple transcript isoforms | Ma et al., 201450 |
| RiboTaper | Identification of translated regions based on 3-nucleotide periodicity | Dunn and Weissman, 201651 |
| Ribotricer | Identification of translating ORFs based on 3-nucleotide periodicity | Oyama et al., 200752 |
| RiboWave | Uses wavelet transform and 3-nucleotide periodicity to located the P-site | Calviello et al., 201653 |
| RiboCode | De novo annotation of the translatome using 3-nucleotide periodicity | Raj et al., 201654 |
| DeepRibo | Neuronal network using ribo-seq data to determin binding patterns and translation initiation sites | Xiao et al., 201855 |
| riboHMM | Identification of coding sequences based on abundance and codon pediodicity | Xu et al., 201856 |
Compilation of different bioinformatic tools, divided according to sequence prediction and ribosome profiling methods, used for the predictions and identification of small open reading frames.