There are numerous bioinformatics tools which predict the targets of a given miRNA. Is there any tool/ software to find the microRNAs regulating a given set of known genes/ mRNAs?
You can get experimentally obtained miRNA binding sites on UTRs/ list of regulated mRNA for a given miRNA through AURA (http://aura.science.unitn.it)
Hi
Many tools to do that. I agree with Andreas about Mirwalk. You have many others compiled in my humble webpage miRNAtools 2.0
http://sites.google.com/site/mirnatools2
By the way, Erik... Great tool AURA !... I will include it in my webpage.
Good luck. Cheers
Paco
Thanks Andreas Dix, Erik Dassi and Francisco Enguita for the reply. This would be of great benefit for me.
By the way, good compilation, Francisco Enguita.
You may find this list useful aswell:
http://journal.imbio.de/JIBtools/viewtopic.php?f=41&t=121
You can get predicted and validated targets in several tools like miRWalk, miRBase, Target Scan etc.,
miRWalk- http://www.umm.uni-heidelberg.de/apps/zmf/mirwalk/
TargetScan- http://www.targetscan.org
miRanda-http://www.microrna.org
Especially in miRWalk you can get both predicted and validated targets of miRNA and a gene.
All the best
I can suggest you miRTarbase (http://mirtarbase.mbc.nctu.edu.tw), a database of experimentally validated microRNA/mRNA interactions.
Why don't you BLAST the 3'UTR or 5'UTR of your gene of interest against all mature sequences you can find in miRBase of your organism of interest?
You would then need to rank the BLAST hits somehow (e.g.: like TargetScan does).
This might be faster than trying many existing tools.
@Jens
BLAST is not enough. Applications for miRNA target prediction are not simply sequence alignment tools. miRNA target prediction algorithms take into account the seed sequence, and compensatory binding-sites. Also the majority of them use the delta-G function of the RNA-RNA hybrid to rank among solutions. The most advanced applications are also able to consider the potential secondary structures of the target mRNA which may prevent miRNA binding.
Best. Paco
@Jens
As Francisco pointed out, BLAST may not be enough. Also, I am not doing it for a single gene. There are a set of genes for which, I need to find the miRNAs. I also used miRTarbase to find the experimentally validated mRNA-miRNA interactions.
miRNA seed region which is complementary to mRNA can be 2-8 nucleotides in length. So some times two nucleotides complementarity can repress the translation of a target mRNA. So I dont think that BLAST is the proper way to find targets of an miRNA and vice versa. Other parameters are also accountable in target prediction. The thermodynamic stability of the mRNA and miRNA duplex along with probability of the formation of secondary structure surrounding the miRNA etc., So it is better to use the tools in target prediction which can give you the targets based on several parameters.
You may find more information about miRNA target prediction here:
http://www.ncbi.nlm.nih.gov/pubmed/24272439
i need the same, i found MicroInspector , a web-based tool to screen the mRNA for detection of miRNA binding site but it doesn,t work these days and i dont know why ? however, as Erik said you can use http://aura.science.unitn.it/ and microRNA.org
good luck
How about RNA22 (https://cm.jefferson.edu/rna22/)?
Or just plain old RNAHybrid in Vienna RNA tools package?
Try also the old good TargetScan: http://www.targetscan.org/vert_72/
Just to provide another answer for anyone looking at this in 2019; a handy tool I use is from DIANA: http://diana.imis.athena-innovation.gr/DianaTools/index.php?r=microT_CDS
You can paste in your list of genes and it will return provide a resulting predicted list of microRNAs.
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