| miRBase is the primary online repository for all microRNA nomenclature, sequences and annotation. This database provides genomic location of miRNAs, miRNA clusters and search or BLAST for precursor and mature miRNA sequences. miRBase mapped reads from short RNA deep-sequencing experiments to microRNAs and users can view these mappings. |
| Stem loop structure and deep sequencing Search miRNAs by genomic location Search of miRNA clusters Search of homolog miRNAs in other species |
| CoGemiR purpose to offer an overview of the genomic organization of microRNAs and of its extent of conservation during evolution. The database collects information on genomic location, conservation and expression data of both known and newly predicted microRNAs and displays the data by benefitting a comparative point of view. The database includes a microRNA prediction pipeline to annotate microRNAs in recently sequenced genomes. |
| Pre-miRNA and mature sequence Expression data in different tissues Tissue specificity |
| The microRNAviewer web-server includes all known miRNAs of currently fully annotated animal genomes in a visual ‘birds-eye’ view representation. microRNAviewer provides a graphical outlook of the current miRNA world together with sequence alignments and secondary structures of each miRNA. |
| miRNA alignment and finding mismatches miRNA genomic location |
| miRNEST 2.0, a comprehensive database of animal, plant and virus microRNAs which is complemented with our extensive miRNA predictions from deep sequencing libraries, data from plant degradome analyses, results of premiRNA classification with HuntMi and miRNA splice sites information. |
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Collection of animal, plant and virus microRNAs |
| The miROrtho database presents the results of a comprehensive computational survey of miRNA gene candidates across the majority of sequenced metazoan genomes. This database was designed and applied a three-tier analysis pipeline: (i) an SVM-based ab initio screen for potent hairpins, plus homologs of known miRNAs, (ii) an orthology delineation procedure and (iii) an SVM-based classifier of the ortholog multiple sequence alignments. The web interface provides direct access to putative miRNA annotations, ortholog multiple alignments, RNA secondary structure conservation, and sequence data. |
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Genomic location both known and predicted miRNAs |
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miRNA expression |
| miRvar have comprehensively curated genetic variations in miRNA loci in the human genome and established a computational pipeline to assess potential functional consequences of these variants along with methods for systematic curation and reporting of variations in these loci. |
Genetic variants of miRNAs and its functional results
| miRiadne, a web tool to harmonize miRNA nomenclature, which takes into account the original miRBase versions from 10 up to 21, and annotations of 25 common profiling platforms from nine brands that manually curated. miRiadne uses the miRNA mature sequence to link miRBase versions and/or platforms to prevent nomenclature ambiguities. |
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A tool for re-annotating miRNA name lists or datasets |
| miRNAfe is a comprehensive tool to extract features from RNA sequences. The user only needs to load a file containing the input sequences and select the features to extract and obtains a text file with the features extracted, which can be used to analyze the sequences or as input to a miRNA prediction software. The tool can calculate up to 80 features which have been divided into six pre-defined groups. |
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A tool for RNA sequences features extraction |
| mirPub is a database with a powerful and intuitive interface, which facilitates searching for miRNA literature, addressing the aforementioned issues. To provide effective search services, mirPub applies text mining techniques on MEDLINE, integrates data from several curated databases and exploits data from its user community following a crowdsourcing approach. This database includes a visualization service that illustrates the evolution of miRNA data, tag clouds summarizing the relevance of publications to particular diseases, cell types or tissues. |
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Information about the correlation of microRNAs to any diseases, tissues and genes |
| miTRATA, the first web-based tool for microRNA Truncation and Tailing Analysis--the analysis of 3' modifications of microRNAs including the loss or gain of nucleotides relative to the canonical sequence. miTRATA employs parallel processing modules to enhance its scalability when analyzing multiple small RNA (sRNA) sequencing datasets. It utilizes version 21 miRBase and its strengths lie in biologist-focused web interface, improved scalability via parallel processing and uniqueness as a web tool to perform microRNA truncation and tailing analysis. |
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Analysis of 3′ modifications of microRNAs |
| PNRD plant ncRNA database provide a way to do fundamental research on plant ncRNAs. Specifications in PNRD are not only the larger amounts of data, but also better service, such as a more user-friendly interface, more multifunctional and browsing options and more background data for users to download. We also integrated currently prevalent technologies and toolkits to strengthen the capability of the database and provide a one-stop service for scientific users. |
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Including literature mining, experimental targets, predicted targets |
| VIRmiRNA is the first specialized resource of experimentally proven virus-encoded miRNAs and their associated targets. It includes VIRMIRTAR viral miRNA target genes and AVIRMIR antiviral miRNAs encoded by the host against viruses. This database would enhance the understanding of viral/host gene regulation and may also prove beneficial in the development of antiviral therapeutics. |
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Including VIRmiRNA, VIRmiRtar and AVIRmir subdatabases |
| Single resource target prediction |
| Artificial microRNAs (amiRNAs) are 21mer small RNAs, which can be genetically engineered and function to specifically silence single or multiple genes of interest in more than 90 plants, according to the previously determined parameters of target gene selection. WMD3 uses your favorite gene(s), which you want to silence, and designs 21mer amiRNA sequences. You will retrieve oligo sequences to express the small RNA from endogenous miRNA precursors. |
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Platform requires only selection of favorite candidates according to a small set of criteria |
