Validated microRNA target sequences

Question

[dolevrahat]

Hi There

I am looking for sequences of validated microRNAs targets (such as the ones in TarBase).

My intention is to subsequently use these sequences in order to attempt to predict the microRNA binding motif using motif prediction tools such as MEME. I could of course take the list of validated targets from TarBase and get the sequence for their entire 3'UTRs from UCSC, but I was hoping for more specific sequences (plus, using the whole 3'UTR may be problematic due to MEME sequence size restriction)

Is there any way to get the sequences for validated targets (from Tarbase or otherwise).

Thanks in advance

Dolev Rahat

[Devon Ryan]

Are you running into problems with the various miRNA target predictors that already exist that you want to write your own? Those already try to determine an approximate target sequence from the miRNA sequence.

[dolevrahat]

@Devon Ryan: Thanks for your answer. The problem is that my project involves searching for targets of a given set of miRNAs across many genomes, whereas the existing tools are mostly oriented towards a small set of well researched genomes. I tried using RNAHybrid and FindTar3 and run into the predictable problem of filtering the results. Theoretically I could resolve this using a threshold on free energy. However, Since I assume that hybridization energy distributions may vary between species I do not want to rely on filtering on the basis of free energy alone. This is why I want to intersect between the output of the energy oriented tools and a putative motif.

Answer 1

[Charles Warden]

1. If you want to predict a motif, you will need to have several sequences. If you limit yourself to validated sequences, you may only find a handful of validated targets per miRNA (at least in most cases).
2. As one option, I am almost certain you can download this information for TargetScan predictions (or, at least get the positions, so that you can download the sequences from the UCSC Genome Browser)

They are not validated, but they give you more to work with. However, my guess is that you would probably recover the seed sequence, which you can figure out without doing any motif finding (although this may also happen if you choose the validated sequences, assuming a large enough number of targets have been validated).

[dolevrahat]

Thank you, will try that