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 database is a new resource of predicted miRNA targets in animals. The latest release is
version 11.0. - 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 Prediction Tools
- 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
- These are the most recent TargetScanS predictions (April 2005). They are essentially the 3'UTR targets reported in the Lewis et al., 2005 paper, with a few changes arising from updated gene boundary definitions from
the April 2005 UCSC genome browser mapping of RefSeq mRNAs to the hg17 human genome assembly. To avoid difficulties in browser display, the few predictions spanning splice junctions are excluded.
- RNAhybrid
is a tool for finding the minimum free energy hybridisation of a long and a short RNA. The hybridisation is performed in a kind of domain mode, ie. the short sequence is hybridised 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 analysing 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 speceis.
- 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 parametrization 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.
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