There are several target prediction tools but they are limited in terms of options that we can select humans, mouse etc genomes. What if the genome sequence of any other organism, which is not listed, in this case how can we possibly predict miRNAs interaction/binding sites within genome of interest?
Hi Azeem... I am afraid that if you are working with "exotic" genomes out of human, mouse, rat or zebrafish you are in trouble. Of course you always have solutions based on handicraft.
I used to employ MiRanda algorithm installed locally in a Linux box. MiRanda takes two files in FASTA format, one with the 3'-UTR sequences and other with the mIRNAs predicting targets. So you can use the genome that you want.
http://www.microrna.org/microrna/getDownloads.do
The main drawback is that you are using just one prediction algorithm... I have used with success to predict targets in genomes from protozoans for instance.
Good luck. Let me know if I can help
Cheers.
Paco
Dear Azeem, Below is the link for designing of artificial microRNA, Target search, and also for generation of oligos that can be used for generation of amiRNA.
http://wmd3.weigelworld.org/cgi-bin/webapp.cgi
Good luck.
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