Microtar is a microrna target prediction program based on mrna sequence complementarity 3utr seed matches and rna duplex energy prediction, assessing the impact of microrna binding on complete mrna molecules. These optional programs can be replaced by similar software. In addition, plant mirna stemloops vary remarkably in length ni et al. Psrnatarget incorporates recent discoveries in plant mirna target recognition, e. Computational prediction of plant mirna targets article pdf available in methods in molecular biology clifton, n.
Existing plant mirna prediction tools lack a crossspecies conservation filter and etm prediction function. All the plant mirna sequences were extracted from the mirbase repository 6. To extend mirdeep2 for plant mirna prediction, parameters are welladjusted according to the statistical characteristics of plant mirnas 5,9,11. If you are looking for mirna annotations based on homology to known mirnas from other plants, you could try microharvester, although i dont know if their web server it still running, it was down just now when i checked if you are looking for mirna annotations from referencealigned small rnaseq data, there are lots of choices, including shortstack, mirdeepp, mirdeepfinder, and mircat.
Prediction of plant premicrornas and their micrornas in. Both sequence homologs or structural homologs of regulatory rna motifs can be identified. One of the advantages by using mirdeepp for plant mirna prediction is that the analysis does not depend on the availability of reference genomes 19. Whenever possible, cdna gene sequences were used for the prediction, as plant mirnas can also bind within utr regions. Targetscan targetscans predicts biological targets of mirnas by searching for the presence of conserved 8mer and 7mer sites that match the seed region of each mirna. The mirtour software has a user friendly webinterface which provides a comprehensive pipeline for identification of plant mirna homologs. Given a mature mirna sequence from a plant species, the system thoroughly searches for potential complementary target sites with mismatches tolerable in mirna target recognition. Pdf computational prediction of plant mirna targets. It uses the rnalib library from the vienna rna package animals.
The tool allows systematic search for mirna complementary targets in any plant whose genome sequence or a large number of expressed sequence tags ests. Prediction of plant premicrornas and their micrornas in genomescale sequences using structuresequence features and support vector machine. Use this resource to query multiple mirnas in one step to find associations between target genes and the mirnas. The tool is primarily meant as a means for microrna target prediction. School of computer science and technology, dalian university of technology, dalian, liaoning 116023 china. Tarhunter, a tool for predicting conserved microrna targets and. A webbased integrated computing system, miru, has been developed for plant mirna target gene prediction in any plant, if a large number of sequences are available. However, most of these methods were designed for mammalian mirna prediction, and few are available for predicting mirnas in the premirnas of specific plant species. Although several prediction tools are available for metazoan genomes. The server allow to perform searches by mirna or target gene. Microrna target prediction mirtar is a tool that enables biologists easily to identify the biological functionsregulatory relationships between a group of knownputative mirnas and protein coding genes. In this regard, specific parameters were introduced into the prediction tools for plant mirnas, such as mirdeepp and mirplant. Recently, prediction methods based on machine learning have been widely used for mirna prediction.
Mirinho a novel alternative to a classical folder based on a thermodynamic nearestneighbour nn model for computing the free energy and predicting the classical hairpin structure of a premirna. The program automates all the steps of mirna similarity search, mirna precursor selection, target prediction and annotation, each of them performed with the same set of input sequences. Microrna database and target prediction tool index abcam. A powerful tool for plant mirna target prediction and pare validation. All the precomputed results are raw, in the sense that they are not filtered according to any cutoff values. Diana microt analyzer a tool for prediction of microrna targets. Regrna is an integrated web server for identifying the homologs of regulatory rna motifs and elements against an input mrna sequence.