MicroRNA Target Prediction
- a database to predict miRNA targets for many vertebrate species.
There are several major changes in the revised database:
i) Updated miRNA annotations and classifications of their conservation level
ii) Heavily revised annotations of 3' UTRs, integrating evidence from RefSeq, Ensembl/Gencode, and experimental datasets measuring 3' UTR isoform abundance
iii) Improvements in the underlying prediction algorithms
- miRanda - microRNA Target Detection
(Memorial Sloan-Kettering Cancer Center)
- 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.
- IANA microT
- iana microT 4.0 is a program for miRNA target prediction which is based on Artificial Neural Networks. It may be used to search for target genes of annotated or user defined miRNA sequences.
- miRBase Target Database
- Searchable database of miR targets on 3' UTR of genes in almost all genomes. Search can be done using miR id, gene name, EnsEMBL id, and keywords. But it does not accept user sequence input.
(BidLab, Institute of Bioinformatics, National Chiao Tung University , Taiwan)
- miRTar is a web server which provides an intuitive interface to allow user input any miRNA/siRNA sequence for identifying miRNA targets against the 3'-UTR of mRNA of mammalian genes. The main advantage of the web server comparing to previously developed tools (see references) is the efficient performance. Thus, the miRNA/siRNA targets search becomes faster enough to be a web server. miRTar incorporates a preprocessing algorithm, named iScan, and a powerful miRNA targets search tool, miRanda, to search the miRNA targets against the most conserved 3' UTR sequences from UCSC Genome Browser.
- miRU: Plant microRNA Potential Target Finder
(Plant Biology Division, The Samuel Roberts Noble Foundation)
- 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.
(Max Delbruck Centrum, Berlin)
- PicTar is an algorithm for the identification of microRNA targets. This online tool provides search function for microRNA targets on mRNA. Search can be done by microRNA or gene name.
(Department of Biological Science and Technology, National Chiao Tung University, Taiwan)
- RegRNA is an integrated web server for identifying the homologs of Regulatory RNA motifs and elements against an input mRNA sequence. For microRNA target prediction, users can input a gene id or name, or a mRNA sequence, the program will scan the input sequence for targets of internally stored human microRNAs. Results are returned in table and graphic view.
- RNA22 microRNA target detection
- Given a microRNA and a mRNA sequence, the program returns microRNA targets on the sequence. A downloadable utility that allows you to install on your local computer and run batch queries (i.e. many microRNAs against many candidate target sequences). It is easy to install, set up and use. It also provides precomputed predictions for several organisms for downloading.
(Universitat Bielefeld, International NRW Graduate School in Bioinformatics and Genome Research)
- 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.