Mirna Target Prediction
I am trying to predict targets for miRNA. The potential targets are ESTs derived from 454 sequencing and the species of interest (a non-model insect) doesn’t have an annotated genome. I am planning to use Targetspy program (http://www.targetspy.org/). The problem that I have is how do I predict the 3’ utrs from the EST sequences? I would appreciate your thoughts.
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I think you should start by predicting ORFs in the ESTs, when you'll have them you'll get the UTRs
To further Asaf's point -- are your ESTs likely to be whole transcripts?
Thanks for your comments Asaf and Qdjm. ORF prediction is a good suggestion. However, most of the sequences may not be whole transcripts as they are derived from 454 data.
I wouldn't confound the target prediction with another imperfect prediction. Afaik (lacking a tidbit of evidence), miRNAs do not only target 3'UTRs but can target anywhere on the mRNA. As a conclusion the UTR/ORF prediction is not beneficial.
I'm at a similar place with my miRNA research - trying to predict targets for a non-model insect using 454 sequencing reads. Did you find a way to do this?