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 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.
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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