miRNA prediction on a given mRNA - (Feb/16/2011 )

Hey Folks,

I am doing research on the miRNA field mostly in wet lab. Nevertheless, I am starting to do some miRNA target predictions in silico before doing it in vitro. I have a couple of mRNAs that I am interested in and would like to know if they are under miRNA regulation. Does anyone know where I can paste a 3'UTR sequence and find out which miRNAs can anneal and may regulate this given miRNA. I am using zebrafish as a model system.
I hope I was clear enough and thanks by advance if you can help me!

Amélie

There are many databases with pre-predicted targets for miRNA but it seems none of them includes zebrafish. Alternatively, you can obtain the miRanda program to run the prediction on your computer. You just need to have the sequences for the miRNA and the 3UTR. The program can be downloaded from here: http://cbio.mskcc.org/research/sander/data/miRNA2003/miranda_new.html

or direct link http://cbio.mskcc.org/research/sander/data/miRNA2003/src/jmiranda/

I personally like using TargetScan because it takes into account conservation of sequences across species. Its also user friendly and can predict miRNA to target and vice versa.

Also, Diane Lab isn't bad because it accumulates data from different miRNA target predictor programs online.

Yes, TargetScan is another nice program which puts a lot of weight on conservation. But there seems not to have a stand-alone program allowing you to run your own prediction.

pcrman on Fri Feb 18 02:35:57 2011 said:

The perl scripts are at the bottom of the page: http://www.targetscan.org/cgi-bin/targetscan/data_download.cgi?db=vert_50

Earnest on Wed Mar 30 18:20:34 2011 said:

Sorry I missed that. Nice find!