Hi! I am now working on miRNAs and I just new to this area.
For the target prediction, since there are several databases and these are based on different algorithms. I just want to know would it necessary to use 2 or more databases for target prediction and use only the intersected targets for downstream analyses, or just do the target prediction from only 1 database is enough?
Thanks
It is always better to use more than one prediction tool. As you rightly pointed out different tools follow different algorithms. While some rely on seed complementarity other make use of binding energy. Species conservation is also important.
You may use miRWalk ( http://zmf.umm.uni-heidelberg.de/apps/zmf/mirwalk/ ) or DIANA tools. Both of them provide information whether the gene target is predicted by other tools or not.
Hi I agree completely with above suggestions. We also use miR-walk. It compares several algorithms. My suggestion is then to combine with real exp.. such as CLIP, RIP or proteomics. Good luck D.
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