We identified conserved and novel miRNA from my plant samples (non model plant). The targets were predicted through psRNA target using Arabidopsis as the background reference but targets were not obtained for some miRNAs. Can i use another reference available at psRNA target particularly for those miRNAs? Is that a proper way using two or more references for target prediction or should move with Arabidopsis alone?
I think miRNA target prediction in plants is more straightforward than in animals, as it require a perfect match between miRNA and its target. I am not sure what do you mean by "background reference" . Are you trying to predict miRNA target at a whole genome level? Or you're interested in specific genes?
It will be better if u use miRNA sequences of your plant. If psRNA target does not produce targets for ur given sequence then use sequence of a closely related species of ur plant. If no targets are predicted for the sequence of closely ralated plant then go for Arabidopsis thaliana. Hope it will be helpful
Thank you Shuai chen, Background reference means the transcript i have selected for target prediction and i am not going behind specific genes. I wanted to know can we depend on more plant transcriptomes for target prediction.
Thank you Iftekhar for your suggestion.
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