I am trying to identify possible microRNA targets in the genome of a non-model insect using miRanda. I have results, but I don't really know what is considered a good score. I'd love to know what would be a reasonable cut off for the score threshold and/or energy threshold so I can, hopefully, eliminate some of the results.
Hi Julie,
Does your species has a well annotated genome? Are you interested in one miRNA or you're trying to predict targets for all miRNAs in you species. Let us know.
Hi Shuai,
The genome for my species is still in draft form, so not well annotated.
I'm currently interested in 5-10 different miRNAs that I've identified as being deferentially expressed in two different developmental of my fly species.
Hi Julie,
It is a little tricky if the genome is not well annotated, which happened to my species too. As you might read my unpublished miRNA target prediction paper. I development my own pipeline to predict miRNA targets based on thermodynamics and on evolutionary conserved 3'UTRs. I think I can modify my pipeline to fit your genomic data and predict miRNA targets for your species. I've sent you a Researchgate message with my email. Please let me know if you are interested in this pipeline. Best,
I have a similar problem. I am working on non-model insect and identified the miRNA in the genome. Now, want to predict the target of identified miRNAs in the genome. Could you suggest me the tool/pipeline for this. Thanks.
I've been playing with miRanda, TargetScan Fly and miRpath and have identified a lot of putative targets. These are all based on the Drosophila genome, so I don't how well they will work for you. My insect is close enough to Drosophila for these tools to be a good starting place. Of course, now I need to do the hard work of verifying these targets which seems to be a pretty complicated process.
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