Table 1.
Evaluation tools/software of sORF translation by ribosomal profiling methods.
| Tool | Feature | Availability | Ref. |
|---|---|---|---|
| ORF-RAETER | Translated ORF identification and quantification based on linear regression. | https://github.com/alexfields/ORF-RATER.githttps://github.com/alexfields/ORF-RATER | [47] |
| Ribo-TISH | A comprehensive toolkit for analyzing TIs and predicting putative ORFs. | https://github.com/zhpn1024/ribotish.git | [56] |
| Ribowave | ORF prediction, protein abundance estimation, TE calculation, and ribosomal frameshift identification based on wavelet transform. | https://ribowave.ncrnalab.org/ | [50] |
| RiboORF | ORF identification based on the arrangement of the ribosome A site, the 3 nt periodicity, and the consistency between codons. | https://github.com/zhejilab/RibORF.git | [51] |
| RiboHMM | ORF identification based on the total abundance and periodic codon structure in RPF. | https://github.com/djf604/RiboHMM.git | [57] |
| ORFquant | ORF prediction and quantification based on multi-taper method. | https://github.com/lcalviell/ORFquant/releases/tag/1.02 | [49] |
| Ribotricer | ORF prediction based on three-nucleotide periodicity. | https://github.com/smithlabcode/ribotricer/releases/tag/v1.3.3 | [58] |
| PRICE | Resolving overlapping sORFs and noncanonical translation initiation based on machine-learning model. | https://github.com/erhard-lab/price.git | [59] |
| Ribocode | De novo assembly and annotation for translatomes based on Wilcoxon signed-rank test. | https://github.com/xryanglab/RiboCode.git | [52] |
| RiboTaper | ORF identification based on the characteristic three-nucleotide periodicity of Ribo-Seq. | https://ohlerlab.mdc-berlin.de/software/RiboTaper_126/ | [48] |
| RP-BP | ORF prediction based on unsupervised Bayesian approach. | https://github.com/dieterich-lab/rp-bp.git | [60] |
| SPECtre | ORF prediction based on 3 nt periodicity. | https://github.com/mills-lab/spectre.git | [61] |
| RiboToolkit | Ribo-Seq web application for analysis and implementation of a full ORF prediction pipeline. | http://rnainformatics.org.cn/RiboToolkit/analysis.php | [62] |
| GWIPS-Viz | Online web server for visualizing processed Ribo-Seq data. | https://gwips.ucc.ie/ | [63] |
| Trips-Viz | https://trips.ucc.ie/ | [64] |