* Diana Micro-T: excellent server for miRNA target prediction in silico, with a friendly user interface. The user can predict targets using miRNAs or putative target gene sequences as input.

* MirPath: data mining server for the analysis of pathways controlled by a subset of miRNAs. It is the first server to combine biochemical data with miRNA regulation and the analysis of both factors together constitutes a huge source of information about the implication of miRNAs in biological processes. Very nice interface and easy to interact with.

* Microinspector: server for the analysis of potential target sites for miRNAs. The user can input the sequence of the 3'-UTR of the gene of interest, and the server will show the potential miRNA binding sites using the most recent MiRbase version. Several parameters for the target binding can be customized by the user.

* MaMi: classical server for the analysis of hybridization energies and structures between miRNAs and target sequences. Chemical parameters can be modified by the user.

* miRecords: integrative resource for the target analysis in silico. It combines results from other applications and servers together with bibliographical information about target prediction and validation.

* mirDIP: integrates twelve microRNA prediction datasets from six microRNA prediction databases, allowing users to customize their microRNA target searches. Combining microRNA predictions allows users to obtain more robust target predictions, giving you more confidence in your microRNA targets.

* miRGator: is a web tool for functional interpretation of miRNAs, integrating functional analysis, expression profile and target prediction to infer physiological roles of miRNAs.

* Magia: integrated gene analysis tool for the cross-determinations of miRNA, targets and gene expression. The server allows the analysis of miRNA and genes expression profiles by adopting different statistical measures of profiles relatedness and algorithms for expression profiles combination.

* Targetscan: classical software for miRNA target prediction. The server allow to perform searches by miRNA or target gene.

* miRTar: MicroRNA Target prediction (miRTar) is a tool that enables biologists easily to identify the biological functionsregulatory relationships between a group of known/putative miRNAs and protein coding genes. It also provides perspective of information on the miRNA targets on alternatively spliced transcripts.

* miRTrail: allows you to easily analyse for potential relationships between a set of miRNAs and a set of mRNAs. This enables you to assess possible important implications of the miRNAs on the given disease.

* Diana Micro-T: excellent server for miRNA target prediction in silico, with a friendly user interface. The user can predict targets using miRNAs or putative target gene sequences as input.

* MirPath: data mining server for the analysis of pathways controlled by a subset of miRNAs. It is the first server to combine biochemical data with miRNA regulation and the analysis of both factors together constitutes a huge source of information about the implication of miRNAs in biological processes. Very nice interface and easy to interact with.

* Microinspector: server for the analysis of potential target sites for miRNAs. The user can input the sequence of the 3'-UTR of the gene of interest, and the server will show the potential miRNA binding sites using the most recent MiRbase version. Several parameters for the target binding can be customized by the user.

* MaMi: classical server for the analysis of hybridization energies and structures between miRNAs and target sequences. Chemical parameters can be modified by the user.

* miRecords: integrative resource for the target analysis in silico. It combines results from other applications and servers together with bibliographical information about target prediction and validation.

* mirDIP: integrates twelve microRNA prediction datasets from six microRNA prediction databases, allowing users to customize their microRNA target searches. Combining microRNA predictions allows users to obtain more robust target predictions, giving you more confidence in your microRNA targets.

* miRGator: is a web tool for functional interpretation of miRNAs, integrating functional analysis, expression profile and target prediction to infer physiological roles of miRNAs.

* Magia: integrated gene analysis tool for the cross-determinations of miRNA, targets and gene expression. The server allows the analysis of miRNA and genes expression profiles by adopting different statistical measures of profiles relatedness and algorithms for expression profiles combination.

* Targetscan: classical software for miRNA target prediction. The server allow to perform searches by miRNA or target gene.

* miRTar: MicroRNA Target prediction (miRTar) is a tool that enables biologists easily to identify the biological functionsregulatory relationships between a group of known/putative miRNAs and protein coding genes. It also provides perspective of information on the miRNA targets on alternatively spliced transcripts.

* miRTrail: allows you to easily analyse for potential relationships between a set of miRNAs and a set of mRNAs. This enables you to assess possible important implications of the miRNAs on the given disease.

Designer of Small Interfering RNAs—DSIR’ (http://biodev.extra.cea.fr/DSIR/DSIR.html)

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3182075/ this can be helpful

Dear Jinsha,

You can follow given link, you may find again many tools:

http://crdd.osdd.net/rna.php

TargetScan : is one of the best for prediction but it is always advisable to use consensus of 2 -5 softwares that uses different parameter for target prediction ..

Hi,

DIANA-microT-CDS (http://62.217.127.8/DianaTools/index.php?r=microT_CDS/index) is the latest version of the microT algorithm. It is currently the only algorithm available that reports MREs on Coding Sequences as well as on 3UTR and it has a great interface.

If you are interested in experimentally validated miRNA targets then DIANA-TarBase v6.0 (www.microrna.gr/tarbase) is the largest collection you can find at the moment (more than 65000 targets in a plethora of species).

The software give many targets with respective score....how many one should consider for its analysis

My suggestion : use as many as possible tools (different tools use different algorithms and are based on different observations/rules) and compare - while having in mind that prediction tools only predict the possibility (based on different requirements) of a gene being a target for specific miRNA (or vice-versa). Even though the biggest issue of prediction tools is usually high (extremely high) false positive rate, on the other hand there is a lot of information on validated targets that have failed being predicted by (any) prediction tools.

you can also try

mirwalk or mirrecords tools/databases (note that using different versions of even the same tool can differ in target prediction)

You can also try miRDB, which was developed by analyzing thousands of miRNA-target interactions from high-throughput sequencing experiments. Common features associated with miRNA target binding have been identified and used to predict miRNA targets with machine learning methods. miRDB hosts predicted miRNA targets in five species: human, mouse, rat, dog and chicken. 

what tool you suggest for entering a custom sequence, not annotated sequence, non-UTR, or DNA sequence to see if there is any interaction with known miRNAs?

Dear sir..... I am also want to predict viral miRNAs..but i couldnt got Vmir analyzer software...can any one pls send me the file of that software for me....my mail i.d is [email protected]