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Most other tools only provide a score of the result's significance which is also provided by miRanda-mirSVR. Although it applies a conservation filter, it does allow for poorly conserved targets. Similar to miRanda-mirSVR, it also considers the additional feature of A-U content in the regions flanking the seed region.

Among the remaining target prediction tools reviewed, miRanda is still a widely-used tool even though it needs to be downloaded to be used and it lacks the additional mirSVR score available in miRanda-mirSVR, which may be desirable.

TargetMiner requires a user-supplied input file and the tool output is limited to seed match characterization. RNAhybrid requires an advanced user due to user-supplied input, adjustment of complex settings, and lack of default values for novice users. The web version of PITA is based on data that is over 5 years out of date, but a downloadable version compatible with user-provided data is available as an alternative option.

The final two remaining reviewed tools, SVM-based MirTarget2 and SVMicrO, are machine-learning tools which hold the promise of learning the subtle contributions of many individual features and using them to make more accurate predictions. As more of these features are elucidated and as more positive and negative targets are validated, the promise of machine-learning approaches to use these features to accurately predict targets comes closer to fruition. At present, these last two machine-learning tools do not display a clear advantage over the tools reviewed above and are inherently limited by the lack of extensive positive and negative data training sets available.

In the future, as we gain more understanding of gene regulation and additional predicted miRNA targets are experimentally validated, we expect that current limitations in miRNA target prediction tools will be addressed. For example, a method was recently proposed that takes advantage of the observation that a miRNA and its target genes are often co-regulated by common transcription factors, which may eventually be incorporated into new or current target prediction tools Fujiwara and Yada, Currently, few of the reviewed target prediction tools are able to address tissue specificity in the prediction of miRNA targets.

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Tools that allow user-provided data, however, can accommodate some level of tissue specificity by incorporating tissue-specific data such as highly expressed miRNAs or miRNA isoforms, tissue-specific mRNA transcript variants, or lists of highly upregulated or downregulated genes.

There is also emerging interest in integrated tools, such as miRmap Vejnar et al. This review highlights the common features of miRNA target prediction and how they are incorporated into different target prediction tools. Further, we encourage the user to be aware of the version, maintenance, and data utilized for each tool.

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By understanding the features and the tools available, the user is well-equipped to choose the most appropriate miRNA target prediction tool available. Sarah M. Peterson, Jeffrey A. Thompson, Melanie L.

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Common features of miRNA target prediction tools There are four commonly used features for miRNA target prediction tools: seed match, conservation, free energy, and site accessibility. Species are specified as part of the miRNA or Ensembl ID, which is somewhat awkward considering that it does not make clear what species are available. Mrs isaacgriberg. Thiago Santana 26 years old 7 1. Any opinions are my own. We accept the following options to complete the test scores requirement by the application deadline:.

Ufkin, and Clare Bates Congdon developed the concept for the structure and content of the manuscript. Thompson, and Melanie L.

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Ufkin contributed equally to the research and initial draft of the manuscript, with guidance from Clare Bates Congdon. Peterson critically revised the manuscript with assistance from Jeffrey A. Thompson and input from Melanie L. All authors reviewed and approved the final version of the manuscript. The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.

The authors would like to thank Dr. National Center for Biotechnology Information , U. Journal List Front Genet v.

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Front Genet. Published online Feb Peterson , 1, 2 Jeffrey A. Thompson , 3 Melanie L. Jeffrey A. Melanie L. Author information Article notes Copyright and License information Disclaimer.

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This article was submitted to Bioinformatics and Computational Biology, a section of the journal Frontiers in Genetics. Received Nov 22; Accepted Jan The use, distribution or reproduction in other forums is permitted, provided the original author s or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

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This article has been cited by other articles in PMC. Keywords: microRNA, target prediction, seed match, conservation, free energy, site accessibility, machine learning, computational approaches. Common features of miRNA target prediction tools There are four commonly used features for miRNA target prediction tools: seed match, conservation, free energy, and site accessibility. Open in a separate window. Figure 1.

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Conservation Conservation refers to the maintenance of a sequence across species. Free energy Free energy or Gibbs free energy can be used as a measure of the stability of a biological system. Figure 2. Less common features of miRNA target prediction tools The features discussed above are those most commonly incorporated into miRNA target prediction tools.

Review of commonly used miRNA target prediction tools In this section, we outline 10 popular miRNA target prediction tools, using the characteristics previously described. Table 11 Summary table of miRNA target prediction tools. Table 1 Profile of miRanda. TargetScan TargetScan Lewis et al. Table 3 Profile of TargetScan.

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Table 5 Profile of MirTarget2. Table 6 Profile of rnaGUI. Table 7 Profile of TargetMiner. A web-based option is available for user-provided sequence data, and a downloadable executable version is available Organisms Humans, mice, flies, and worms User adjustability Seed size, wobble or mismatch, conservation, and inclusion of a flank region Features Seed match, conservation, free energy, site accessibility and target-site abundance. Table 10 Profile of RNAhybrid. Brief summary of tools excluded from this review Space prevents inclusion of an exhaustive listing of miRNA target prediction software, although some of the original miRNA target prediction tools warrant mention, such as Pictar Krek et al.

Discussion Identifying the target of a specific miRNA is one approach for discovering the role of the miRNA in normal or aberrant biological processes. Author contributions Sarah M. Conflict of interest statement The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.

References Ambros V. MicroRNAs and developmental timing. TargetMiner: microRNA target prediction with systematic identification of tissue-specific negative examples. Bioinformatics 25 , — Comprehensive modeling of microRNA targets predicts functional non-conserved and non-canonical sites. Genome Biol. Principles of microRNA-target recognition. PLoS Biol.

Structure clustering features on the Sfold Web server. Bioinformatics 21 , — ComiR: combinatorial microRNA target prediction tool. Nucleic Acids Res. Specificity of microRNA target selection in translational repression. Genes Dev. In-Silico algorithms for the screening of possible microRNA binding sites and their interactions. Genomics 14 , — MicroRNA targets in drosophila. Science , — MicroRNAs: critical mediators of differentiation, development and disease. Swiss Med. Genome Res. BMC Genomics 2 :S3 Weak seed-pairing stability and high target-site abundance decrease the proficiency of lsy-6 and other microRNAs.

MicroRNAs in Cancer. MicroRNA targeting specificity in mammals: determinants beyond seed pairing. Cell 27 , 91— Fast folding and comparison of RNA secondary structures. Using expression profiling data to identify human microRNA targets. Methods 4 , — The role of microRNAs in cancer susceptibility. Human MicroRNA targets. The role of site accessibility in microRNA target recognition.

BMC Bioinformatics 7 Acids Res.


Combinatorial microRNA target predictions.