Table 2.
Most used bioinformatic tools for miRNA/lncRNA sequence-based prediction.
| Name | URL | Applications |
|---|---|---|
| Diana Tools | http://diana.imis.athena-innovation.gr/DianaTools/index.php | A package that provides algorithms, databases, and software for interpreting and archiving data in a systematic framework starting from deep sequencing data, the annotation of miRNA regulatory elements, and targets to define the role of ncRNAs in different diseases. |
| GDCRNATools | http://bioconductor.org/packages/devel/bioc/html/GDCRNATools.html | An R package that provides a standard tool to downloading, organizing, and integrative analyzing of RNA expression data in the Genomic Data Commons (GDC) portal, deciphering mainly the lncRNA-mRNA-related ceRNAs regulatory network in cancer. |
| Microcosm Targets | http://www.ebi.ac.uk/enright-srv/microcosm/htdocs/targets/v5/ | A web resource containing computationally predicted targets for miRNAs across many species, including humans. MicroCosm Targets database uses dynamic programming alignment to identify highly complementary miRNA–mRNA pairs. |
| miRanda | http://www.mirbase.org/ | The miRBase website provides a wide range of information on published miRNAs, including their sequences, their biogenesis precursors, genome coordinates and context, literature references, deep sequencing expression data, and community-driven annotation. |
| miRcode | http://www.mircode.org/ | The miRcode web interface provides basic search functionality for finding putative miRNA–target sites in lncRNAs of interest or predicted targets of specific miRNAs. |
| MiRDB | http://www.mirdb.org/ | An online database able to predict miRNAs target by a bioinformatics tool, MirTarget, which was developed by analyzing thousands of miRNA–target interactions from high-throughput sequencing experiments. |
| miRge | http://atlas.pathology.jhu.edu/baras/miRge.html | MiRge employs a Bayesian alignment approach, whereby reads are sequentially aligned against customized mature miRNA, hairpin miRNA, noncoding RNA, and mRNA sequence libraries. Reads for all other RNA species are provided, which is useful for identifying potential contaminants and optimizing small RNA purification strategies. |
| miRLAB | https://bioconductor.org/packages/release/bioc/html/miRLAB.html | An R package for automating the procedure of inferring and validating miRNA–mRNA regulatory relationships. It includes a pipeline to obtain matched miRNA and mRNA expression datasets directly from TCGA, the functions for validating the predictions using experimentally validated miRNA target data and miRNA perturbation data. |
| miRNApath | https://bioconductor.org/packages/release/bioc/html/miRNApath.html | A package for provision pathway enrichment techniques for miRNA expression data. miRNApath online database uses miRNA target genes to link miRNAs to metabolic pathways. |
| miRTarBase | http://mirtarbase.mbc.nctu.edu.tw/ | A database containing miRNA–target interactions (MTIs). The collected MTIs are validated experimentally by reporter assays, Western blot, or microarray experiments with overexpression or knockdown of miRNAs. |
| PicTar | http://www.pictar.org/ | A computational method for identifying common targets of miRNAs. Through statistical tests using genome-wide alignments of eight vertebrate genomes, PicTar is able to specifically recover published miRNA targets. |
| RegRNA | http://regrna.mbc.nctu.edu.tw/html/prediction.html | An integrated web server to identify homologs of the regulatory RNA motifs and elements against an input mRNA sequence. RegRNA displays prediction results in a graphical interface generated by various integrated analytical tools, and allows users to annotate their own experimental sequences or to discover homologs of their desired motifs. |
| RNA22 | https://cm.jefferson.edu/rna22/ | A pattern-based method for the identification of miRNA binding sites and their corresponding heteroduplexes. |
| starBase v2.0 | http://starbase.sysu.edu.cn/ | A database able to provide: the miRNA-pseudogene interaction networks, interaction maps between miRNAs and circRNAs, ceRNA functional networks based on miRNA–target interactions overlapping with high-throughput CLIP-Seq data, miRNA–lncRNA interactions, and a variety of interfaces and graphic visualizations to facilitate analysis of CLIP-Seq data, RBP binding sites, miRNA targets, and ceRNA regulatory networks in normal and cancer cells. |
| TargetScan | http://www.targetscan.org/ | A web server that predicts miRNA target genes by searching for the presence of 6- to 8-mer sites that match the seed region of a given miRNA and make use of species alignment to locate conserved sites. |
| TargetScore | https://bioconductor.org/packages/release/bioc/html/TargetScore.html | A Bayesian probabilistic scoring method taking into account the fold-change due to miRNA overexpression and sequence-based information. |