Table 2.
Few bioinformatics analysis tools essential for studying the complex functions and interactions of non-coding RNA (ncRNA) molecules.
| Tool | Description | Examples | Refs. |
|---|---|---|---|
| Rfam | RNA family database for both coding and non-coding RNAs | ncRNA families | [43] |
| miRBase | MicroRNA database for sequences, structures, targets, and functions | microRNAs | [47] |
| RNAfold | Software for predicting RNA secondary structures based on thermodynamic principles | lncRNAs, circRNAs | [62] |
| Cytoscape | Software for visualizing and analyzing complex networks | ncRNA-mRNA interactions, regulatory pathways, signaling pathways | [80] |
| CLIP-seq analysis tools | Bioinformatic tools for analyzing CLIP-seq data for RNA-protein interactions | CIMS, PIPE-CLIP, Piranha | [25,68,106] |
| RNAcentral | A unified database for all types of RNA sequences, structures, and annotations | all types of RNAs | [84] |
| lncRNAdb | A database of annotated lncRNAs with information on sequences, structures, and functions | lncRNAs | [75] |
| NPInter | A database of non-coding RNA-protein interactions with experimental evidence | ncRNA-protein interactions | [110] |
| miRNApath | A web-based tool for predicting miRNA-target interactions and functional pathways | miRNA-target interactions, functional pathways | 10.18129/B9.bioc.miRNApath |
| MINTbase | A database of molecular interactions for non-coding RNAs, including miRNAs, lncRNAs, and circRNAs | ncRNA interactions | [73] |
| LncRNA2Target | A web-based tool for predicting lncRNA-mRNA interactions and functional roles | lncRNA-mRNA interactions, functional roles | [41] |
| deepBase | A database of deep-sequencing data for ncRNAs, including miRNAs, lncRNAs, and circRNAs, with annotations and analyses | ncRNA deep-sequencing data | [99] |