miRNA target prediction for non-model-organism

[MichalGordon]

Hi all,
I would like to use one of the programs for miRNA target prediction (e.g. TargetScan, PicTar, DIANA-microT) to analyze my data from non-model organism (fish), However, as far as I can see, I have to choose organism to work on from a (very) limited list.
There is a way to use these programs by insert my 3' UTR fasta file and miRNAs fasta file? Alternatively, there are other programs that allow doing that?
Thank a lot
Michal

[DrOM]

Hi!

I haven't run the script myself so far, but you can download the perl script from the targetscan website. What you will need as an input are two files, a miRNA family file and a multi-alignment file. When downloading the package the Bartel group is providing example files.

I just saw that the website also has prediction for zebrafish

http://www.targetscan.org/fish_62/

..and you can download alignments etc from here

http://www.targetscan.org/cgi-bin/targetscan/data_download.cgi?db=fish_62

Cheers

Pablo

[Wallysb01]

miRanda and RNAhybrid have downloadable versions you can run locally with your own 3' UTRs and miRNAs.