Several articles reports that three target predictor Target Scan, Miranda and PicTar have predicted highest percentage of experimentally validated miRNA targets, but when I looked at their websites, it seems they just adjusted to predict targets for some species (human, chicken, mouse and etc.) and I have a list of miRNAs predicted in turkey (meleagris) and I wonder how can I use these most reliable target predictors?
Could any one help me how can I use these softwares?
Hi Ali,
I suggest you to take a look at this very recent review (link attached) on the computational predictions of microRNA targets in animals.
In particular, the review points to a few methods that do not limit species for which they predict : RNAhybrid, MicroInspector, MicroTar and MIRZA.
Hope this helps.
http://www.ncbi.nlm.nih.gov/pubmed/?term=25471818
Hi Ali,
I suggest you have a look a this old study that should the limits of bioinformatic predictors: http://www.ncbi.nlm.nih.gov/pubmed/18668037
For my miR-181 study, I tested 100+ predicted targets that I have crosslisted from several target predictors. I concluded that computational methods were not yet reliable and had very high false positive rates.
I hope this helps.
Jean-Charles
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- Biological Science
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- microRNA