How to predict targets of unkown miRNAs in Drosophila - (Sep/09/2011 )

Hi everyone,
I have recently got a chance to work on a micro RNA related project and so not very familiar with this stuff. I have some micro RNA sequences in hand that came from deep sequencing analysis. These are novel micro RNAs and do not belong to well known micro RNA families. My task is to find their targets but have no idea from where to start. Are there any softwares that can help in such predictions ? My experimental model is Drosophila. Any suggestions will be of great value.

-hamid-

Hi hamid,
Since you want to predict custom miRNA to target in Drosophila mRNA genes, the following tools may help you:
MiRanda
TargetScanFly Custom search
RNA22

-whitedolphin-

Hi WhiteDolphin. I couldnt reach MiRanda or RNA22 but have tried TargetScanFly. It predicts quite a large number of possible targets and its still hard to know which one will be biologically relevant. I will try to use MiRanda and RNA22 as well. Thank you

-hamid-