Figure 1:
Tools and databases commonly used in the study of non-model organisms’ miRNAs_
| Tool | Description | Access link | Reference |
|---|---|---|---|
| DATABASES | |||
| miRBase | The primary repository for miRNA sequences and annotation. | https://www.mirbase.org/ | Kozomara et al. (2019) |
| MirGeneDB | High-confidence, manually curated miRNA gene database. | https://mirgenedb.org/ | Clarke et al. (2025) |
| Rfam | Database of ncRNA families from a wide array of species. | https://rfam.org | Kalvari et al. (2021) |
| TargetWormScan | Searchable database of predicted regulatory targets of worm miRNAs. | https://www.targetscan.org/worm_52/ | Lewis et al. (2005) |
| PmiREN | Comprehensive plant repository of plant miRNAs. | https://pmiren.com/ | Guo et al. (2020) |
| ncPlantDB | Database specialized in ncRNAs in plants. | https://bis.zju.edu.cn/ncPlantDB/index/ | Liu et al. (2025) |
| ExoCarta | Database containing information on exosomal proteins and RNAs including miRNAs. | http://exocarta.org/index.html | Keerthikumar et al. (2016) |
| miRTarBase | Comprehensive collection of validated miRNA-mRNA targets. | https://mirtarbase.cuhk.edu.cn/~miRTarBase/miRTarBase_2025/php/index.php | Cui et al. (2025) |
| miRecords | Resource for animal miRNA-target interactions including C.elegans. | http://c1.accurascience.com/miRecords/ | Xiao et al. (2009) |
| PREDICTION TOOLS | |||
| MirDeep2 | Most widely used tool for both known and novel miRNA prediction in animals and plants. | https://github.com/rajewsky-lab/mirdeep2 | Friedländer et al. (2012) |
| miRanalyzer | Tool for the detection of known, and prediction of new miRNAs, in high-throughput sequencing experiments. | http://bioinfo2.ugr.es/miRanalyzer/ | Hackenberg et al. (2011) |
| miRPlant | miRNA predictor utilizing plant-specific parameters (e.g., handling of diverse hairpin lengths and sequences). | https://sourceforge.net/projects/mirplant/ | An et al. (2014) |
| sRNAbench | Part of the sRNAToolKit suite for miRNA discovery and quantification using sRNASeq data. | http://bioinfo5.ugr.es/srnatoolbox/ | Aparicio-Puerta et al. (2022) |
| ShortStack | Highly accurate, plant-optimized, and supports multi-mapping small RNAs. | https://github.com/MikeAxtell/ShortStac | Axtell (2013) |
| miRPara | Predicted miRNA precursors based on structural and sequence features. | https://github.com/weasteam/miRPara | Wu et al. (2011) |
| RNAFold | Comprehensive collection of tools for folding, design and analysis of RNA sequences. | http://rna.tbi.univie.ac.at/cgi-bin/RNAWebSuite/RNAfold.cgi | Gruber et al. (2008) |
| TARGET PREDICTION | |||
| miRanda | An miRNA target scanner that aims to predict mRNA targets for miRNAs using dynamic-programming alignment and thermodynamics. | https://github.com/hacktrackgnulinux/miranda | Betel et al. (2010) |
| RNAHybrid | Tool for finding the minimum free energy hybridization of a long and a short RNA. | https://bibiserv.cebitec.uni-bielefeld.de/rnahybrid | Krüger and Rehmsmeier (2006) |
| psRNATarget | Specifically developed to identify target transcripts of plant regulatory sRNAs. | https://www.zhaolab.org/psRNATarget/ | Dai and Zhao (2011) |
| p-TarPMir | Deep learning model adapted for plant miRNA target prediction. | https://ptarpmir.cu-bic.ca | Ajila et al. (2023b) |
| miTAR | Animal trained hybrid deep learning approach to predict miRNA targets. | https://github.com/tjgu/miTAR | Gu et al. (2021) |
Distinguishing characteristics inherent to miRNA and siRNA_
| Feature | miRNA | siRNA |
|---|---|---|
| Origin | Endogenous | Endogenous and exogenous |
| Structure | Hairpin precursor | Long dsRNA |
| Processing enzymes | Dicer1 or DCL1 (in nucleus, mostly) | Dicer2 or DCL4 (also DCL2, DCL3 depending on siRNA class) |
| Target complementarity | Partial (often with central mismatches) or near perfect | Usually perfect or near-perfect |
| Function | Post-transcriptional gene regulation (mRNA degradation or translational inhibition) | Gene silencing, antiviral defense, transposon suppression, RdDM |
| Target specificity | Often targets multiple genes in the same family | Highly specific to one or few targets |