Plant mirna prediction software

Microrna database and target prediction tool index abcam. Regrna is an integrated web server for identifying the homologs of regulatory rna motifs and elements against an input mrna sequence. These optional programs can be replaced by similar software. 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. All the plant mirna sequences were extracted from the mirbase repository 6. The mirtour software has a user friendly webinterface which provides a comprehensive pipeline for identification of plant mirna homologs.

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. 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. Whenever possible, cdna gene sequences were used for the prediction, as plant mirnas can also bind within utr regions. A powerful tool for plant mirna target prediction and pare validation. Psrnatarget incorporates recent discoveries in plant mirna target recognition, e. The server allow to perform searches by mirna or target gene.

For instance, more repeated matching is allowed in reads alignment step since plant mirnas typically possess larger families than the 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. 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. Mirinho has quadratic instead of cubic complexity and is much more efficient also in practice. 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. Diana microt analyzer a tool for prediction of microrna targets. Existing plant mirna prediction tools lack a crossspecies conservation filter and etm prediction function. The tool is primarily meant as a means for microrna target prediction. 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. In this regard, specific parameters were introduced into the prediction tools for plant mirnas, such as mirdeepp and mirplant. Prediction of plant premicrornas and their micrornas in genomescale sequences using structuresequence features and support vector machine.

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. Computational prediction of plant mirna targets article pdf available in methods in molecular biology clifton, n. Tarhunter, a tool for predicting conserved microrna targets and. Prediction of plant premicrornas and their micrornas in. Use this resource to query multiple mirnas in one step to find associations between target genes and the mirnas. 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. 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. Pdf computational prediction of plant mirna targets. 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. School of computer science and technology, dalian university of technology, dalian, liaoning 116023 china.