Can anyone suggest whether we can use Unigene sequence of an organism to identify microRNA targets?
I cannot see a good reason why you could not run microRNA target prediction methods on UniGene sequences.
I couldn't understand your answer. The reason why am raising this question is in psRNAtarget, the database being searched against is Unigene sequences. I have identified few miRNAs sequences, to identify the targets for those miRNAs, am raising this question.
May be these might help.