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This article mainly introduces the use of miRanda and mirSVR tools, has a certain reference value, interested friends can refer to, I hope you can learn a lot after reading this article, the following let Xiaobian take you to understand.

There are many tools to predict miRNA binding sites. The tools represented by TargetScan are accurate for most conservative binding sites. However, some miRNA binding sites are unconventional and not conservative among species, so the prediction of these sites needs to be improved.

MiRanda software determines the miRNA binding site by the following two factors

Degree of sequence complementary matching between miRNA and mRNA

Free energy of the formed composite structure

The schematic diagram is as follows

The possibility of binding sites is evaluated directly according to the score of sequence matching and the corresponding free energy. because it does not depend on the conservation of binding sites, miRNA binding sites can be evaluated more widely.

MirSVR is a scoring mechanism. The binding site predicted by miRanda is scored by a regression model. The lower the score is, the more reliable the binding site is.

Through miRanda and mirSVR, the developers predicted the miRNA collection site information of five common species, including humans and mice, and organized the results into a database at the following URL

Http://www.microrna.org/microrna/home.do

The number of species and miRNA contained in the database is summarized as follows

Database retrieval based on miRNA or mRNA is supported. The search results are as follows

As you can see, there are many results predicted by the software, and there are thousands of candidate target genes in a miRNA. Click view targets to see the corresponding list of target genes and MirSVR values.

The database is downloaded free of charge, as well as downloads of miRanda software, but the source code for the mirSVR scoring system is not yet available.

The basic usage of miRanda software is as follows

Miranda miRNA.fa genome.fa\-sc 150\-en-7\-out target.txt

The first parameter is the sequence of miRNA, the second parameter is the genomic sequence, such as the 3'UTR sequence corresponding to the transcript,-sc specifies the threshold of sequence alignment score, the binding sites less than this threshold will be filtered out, and-en specifies the threshold of free energy, and the result must be less than this threshold.

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