Web Resources
microRNA Sequence Databases
- The miRBase Sequence Database - a searchable database of published miRNA sequences and annotation. The data were previously provided by the miRNA registry.
The miRBase Registry continues to provide gene hunters with unique names for novel miRNA genes prior to publication of results. The miRBase Targets MicroCosm Targets (formerly miRBase Targets) is a web resource containing computationally predicted targets for microRNAs across many species. The miRNA sequences are obtained from the miRBase Sequence database and most genomic sequence from EnsEMBL. The latest release is version 14.0. - The Plant MicroRNA Database - Our PMRD try to integrate the available large information of plant microRNAs data, consisting of microRNA sequence and their target genes, secondary dimension structure, expression profiling, genome browser, etc.
- MSKCC Computational Biology Center - microRNA and their potential targets predicted with miRanda software for human, drosophila, and zebrafish
- Patrocles - a database of polymorphic miRNA-target interactions. Patrocles compiles SNPs in the 3'UTR of human and mouse genes that either create or destroy miRNA target sites. miRNA target sites are defined as octamer motifs that are expected to show perfect Watson-Crick complementarity with the 5' end of mature miRNAs.
- GenomeTrafac - a whole genome resource for the detection of transcription factor binding site clusters associated with conventional and microRNA encoding genes conserved between mouse and human gene orthologs.
- miRDB - miRDB is an online database for miRNA target prediction and functional annotations in animals. All the targets were predicted by a bioinformatics tool called MirTarget2, which was developed by analyzing thousands of genes downregulated by miRNAs with an SVM learning machine. Common features associated with miRNA target binding have been identified and used to predict miRNA targets. miRDB hosts predicted miRNA targets in five species: human, mouse, rat, dog and chicken.
microRNA Functional Analysis Tools
- MMIA (microRNA and mRNA integrated analysis), a versatile and user-friendly web server that integrates miRNA and mRNA expression data with predicted miRNA target information for analyzing miRNA-associated phenotypes and biological functions by gene set analysis, in addition to analysis of miRNA primary transcript gene promoters.
- The miRò Ontology Database - a web-based knowledge base that provides users with miRNA–phenotype associations in humans. It integrates data from various online sources, such as databases of miRNAs, ontologies, diseases and targets, into a unified database equipped with an intuitive and flexible query interface and data mining facilities.
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EXPANDER (EXpression Analyzer and DisplayER) - is a
java-based tool for analysis of gene expression data.
Expander is an integrated software platform for the analysis
of gene expression data, which is freely available for
academic use. It is designed to support all the stages of
microarray data analysis, from raw data normalization to
inference of transcriptional regulatory networks. It
includes microRNA target predictions for Human, Mouse, Fly,
and C. elegans.
microRNA Discussion / General Information
- www.mirnablog.com, …Trying To Keep Track Of Advances In miRNA Research…
- microRNA Discussion Group This group provides a forum for discussions relating specifically to microRNA.
- microRNA Discussion Group - Linkedin
- miRNAtools - This page is a compilation of several tools to analyze miRNA sequences, determine their targets and to analyze their possible roles in cellular metabolism. The user can follow TUTORIALS that show how to extract information on miRNA function by using real and theoretical examples.
microRNA Prediction Tools
- miRecords is resource for animal miRNA-target interactions developed at the University of Minnesota. miRecords consists of two components. The Validated Targets component is a large, high-quality database of experimentally validated miRNA targets resulting from meticulous literature curation. The Predicted Targets component of miRecords is an integration of predicted miRNA targets produced by 11 established miRNA target prediction programs
- PicTar is an algorithm for the identification of microRNA targets. This searchable website provides details (3' UTR alignments with predicted sites, links to various public databases etc) regarding:
microRNA target predictions in vertebrates (Krek et al, Nature Genetics 37:495-500 (2005)) microRNA target predictions across seven Drosophila species (Grün et al, PLoS Comp. Biol. 1:e13 (2005)) A Genome-wide map of miRNA targets in C. elegans (Lall et al, Current Biology 16, 1-12 (2006)) - miRanda is an algorithm for finding genomic targets for microRNAs. This algorithm has been written in C and is available as an open-source method under the GPL. MiRanda was developed at the Computational Biology Center of Memorial Sloan-Kettering Cancer Center. This software will be further developed under the open source model, coordinated by Anton Enright and Chris Sander (miranda@cbio.mskcc.org).
- TargetScan: Prediction of microRNA targets - Release 5.1 (April 2009). TargetScan predicts biological targets of miRNAs by searching for the presence of conserved 8mer and 7mer sites that match the seed region of each miRNA.
- RNAhybrid is a tool for finding the minimum free energy
hybridization of a long and a short RNA. The hybridization is performed in a kind of domain mode,
i.e.. the short sequence is hybridized to the best fitting part of the long one. The tool is primarily meant as a means for microRNA target prediction.
- miRNA - Target Gene Prediction at EMBL - This website provides access to our 2003 and 2005 miRNA-Target predictions for Drosophila miRNAs. Both methods make use of genome comparison across insect species. Our 2005 predictions are based on pairing rules from a systematic experimental study (Brennecke & Stark et al., 2005) and have a very high sensitivity and specificity as assessed by experimental tests (see Supplement in Stark & Brennecke et al., 2005). We thus highly recommend to use the new predictions.
- DIANA MicroT Analyzer - A tool for prediction of MicroRNA targets
- miRScan - Predict miRNA by
analyzing a hairpin sequence
- ProMiR II - Probablistic miRNA Prediction - ProMiR II is an improved version of the
ProMiR for more general prediction of miRNAs. ProMiR II consists of three programs: ProMiR-v, ProMiR-c, and ProMiR-g. ProMiR-v searches both conserved and non-conserved miRNAs in the vicinity of a known miRNA. ProMiR-c predicts both conserved and non-conserved miRNAs in the vicinity of a candidate (70~150 nt). ProMiR-g provides a more general service such as, the prediction of miRNA genes in a long sequence (70 nt~10 kb) of various
species.
- RegRNA - is an integrated web server for identifying the homologs of Regulatory RNA motifs and elements against an input mRNA sequence. Both sequence homologs or structural homologs of regulatory RNA motifs can be identified.
- MicroInspector - A scanning software for detection of microRNA binding sites.
- RNA22 - A pattern-based method for the identification of microRNA-target sites and their corresponding RNA/RNA complexes.
- TargetBoost - MicroRNA target prediction demo.
- MiRAlign - MicroRNA Identification Based on Sequence and Structure Alignment.
- microHARVESTER - microHARVESTER can identify candidate miRNA homologs based on a query miRNA, with excellent sensitivity and specificity. The microHARVESTER takes advantage of the conservation pattern typical for miRNA genes: the (mature) miRNA is most conserved since its sequence is crucial for target interaction; the miRNA* is less conserved but restricted by the need to extensively base-pair with the miRNA; the rest of the miRNA gene can be less conserved.
- miRU: Plant microRNA Potential Target Finder - The program predicts plant miRNA target genes. It reports all potential sequences complementary to the query with mismatches no more than specified for each mismatch type. In addition, each mismatch is penalized according to the mismatch type and position to the miRNA.
- CrossLink - Visualization and exploration of sequence relationships between (micro) RNAs. After a
parameterization phase, CrossLink uses the established tools BLAST, Vmatch and RNAhybrid to determine sequence relationships. Then, nucleotide sequences and their relationships are displayed as nodes and links of a network, respectively. Relationship attributes are reflected by labels and graphical attributes of each link and corresponding alignments pop up on a mouse-click. The type and number of links displayed can be adjusted interactively using value histograms and thresholds - taking a combination of dependencies on different relationship aspects into account. Powerful network layout operations and navigation capabilities complete the visualization features of this tool.
microRNA Analysis from Deep Sequencing Data
- mirTools – a web server for microRNA profiling and discovery based on high-throughput sequencing data.
Classification of the large-scale short reads into known categories, such as known miRNAs, non-coding RNA, genomic repeats or coding sequences. Providing a detailed annotation information of known miRNAs, such as miRNA/miRNA*, absolute/relative reads count and the most abundant tag. Discovery of the novel miRNAs from the high-throughput sequencing technology. Identification of the differentially expressed miRNAs according to read tag counts (the number of reads for each tag reflects relative express level). - miRDeep - Discovering known and novel miRNAs from deep sequencing data. The miRDeep package was developed to discover active known or novel miRNAs from deep sequencing data (Solexa/Illumina, 454, ...). The package consists of everything you need to analyze your own deep sequencing data after removal of ligation adapters: a number of scripts to preprocess the mapped data, and the core miRDeep algorithm that will analyze and score these data.
- deepBase - a database for deeply annotating and mining deep sequencing data. A novel database, developed to facilitate the comprehensive annotation and discovery of small RNAs from transcriptomic data. The current release of deepBase contains deep sequencing data from 185 small RNA libraries from diverse tissues and cell lines of seven organisms: human, mouse, chicken, Ciona intestinalis, Drosophila melanogaster, Caenhorhabditis elegans and Arabidopsis thaliana. For the purpose of comparative analysis, deepBase provides an integrative, interactive and versatile display. A convenient search option, related publications and other useful information are also provided for further investigation.
- miRExpress - Analyzing high-throughput sequencing data for profiling microRNA expression. A systematic method, for extracting miRNA expression profiles from sequencing reads generated by second-generation sequencing. miRExpress contains miRNA information from miRBase and efficiently reveals miRNA expression profiles by aligning sequencing reads against the sequences of known miRNAs. miRExpress can be used to find novel miRNA candidates by aligning reads with sequences of known miRNAs of various species.
- miRanalyzer - A microRNA detection and analysis tool for next-generation sequencing experiments. The web server tool requires a simple input file containing a list of unique reads and its copy numbers (expression levels). Using these data, miRanalyzer (i) detects all known microRNA sequences annotated in miRBase, (ii) finds all perfect matches against other libraries of transcribed sequences and (iii) predicts new microRNAs. The prediction of new microRNAs is an especially important point as there are many species with very few known microRNAs.
- CID-miRNA - Computational Identification of microRNA. A web server for identification of miRNA precursors in a given DNA sequence, utilizing secondary structure-based filtering systems and an algorithm based on stochastic context free grammar trained on human miRNAs. CID-miRNA analyses a given sequence using a web interface, for presence of putative miRNA precursors and the generated output lists all the potential regions that can form miRNA-like structures. It can also scan large genomic sequences for the presence of potential miRNA precursors in its stand-alone form.
- miRCat - miRNA Categoriser. miRCat is a tool to identify miRNAs in high-throughput small RNA sequence data. miRCat takes a FASTA file of small RNA reads as input and will map them to a reference genome. The tool then looks at genomic hit distribution patterns and secondary structure of genomic regions corresponding to sRNA hits and will predict miRNAs and their precursor structures. miRCat has been tested on published datasets.
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